Okay so I've used the donotargue website to generate my ini files to improve LOD and lighting etc. My problem is that everytime i open the skyrim launcher it re-initializes my graphics settings and I can no longer open my save files. The temporary solution is to set them to read-only.....

BUT

When i do i have to manually set the difficulty setting everytime I enter and my FOV settings are not kept...

Is there a way to tell skyrim not to touch my settings without setting ini files as read-only? A flag in the ini perhaps?

Never use an INI file of someone else or an INI file generator that says it will make your settings to what they should be. That's asking for trouble. Always set your settings in game first and then modify it yourself. Deleting your INI files is your best option here.

A way round it would be to launch skyrim from TESV.exe, this will circumvent the skyrim launcher.

As posted though, never use someone else's ini. You get your own, then tweak it yourself.

I right-click my skyrimprefs.ini and skyrim.ini, goto properties, and hit read-only. This way, the launcher doesn't mess with my custom settings. Keep of copy of those files elsewhere just in case.

After each game patch, I delete the my inis, let Steam and game create new ones, then I open up my backups and the new inis with Notepad++ and compare, just to see if Bethesda brought anything new to the table. Mostly, I just replace the new patch inis with my backups and go back to before (unless patch notes specifically said they addressed something my custom tweaks were doing)

The problem is not that the ini settings I use are not working. If I set the file to read-only the game looks fine. BUT skyrim keeps trying to change the settings and setting to read-only blocks me out of changing things within game and also "data files" is greyed out. This did not happen before the previous patch.

Making changes to the ini file manually is impractical because there are several hundred changes that I have made and I do not know the exact values or lines to change. Is there a guide somewhere that would help me make these changes?

Is that really the only solution? Why was I able to use the ini generator before with no issues?

Thats all well and good but if i set the files to read-only i can no longer access the "data files" menu or change the difficulty within the game

http://www.gamesas.com/topic/1308114-the-elder-scrolls-v-skyrim-tweak-guide-from-nvidia/
There's something in the INI files that's not right, that's why it's changing them.
You got lucky. It's the best solution.

Its complaining about what's in the line sD3DDevice="Your video card goes here" in your skyrimprefs.ini file, it doesn't match what its expecting so it'll reset the settings since it expects it'll match going forward.

To fix this I recommend the following path:
Open the skyrimprefs.ini file in notepad.
Run the launcher and let it do its detection thing.
Open the skyrimprefs.ini file again in another notepad.
Find that line I mentioned above.
Make sure your first one's entry for that line matches what the second one has.
Close the second one.
Save the first one.
Done.

(Yah, I met this a lot dealing with the ENB engines since they have several naming schemes)

Beyond that though: that ini generate creates a lot of garbage values that serve no purpose. You'd probably be better off initially building a prefs.ini using the regular launcher, opening it up and comparing to what that engine thing suggests and only changing values in your skyrimprefs.ini file that you can already find in it and do them a few at a time and trying the game out so you get a good idea of what you're actually influencing with each adjustment.

You can change difficulty within the ini manually of course. Do you mean accessing the data files to decide which ones to implement on each launch, or the make sure they load every time? Cause if its the latter, you can use bLoadLooseFiles=1 in the skyrim.ini to help this happen. But if its the former, then I don't think you can do it...I don't see how you can change some launcher settings while keeping your custom stuff and prevent overwriting. Just bypass the launcher as Bigdaddy suggests.

However, you state "because there are several hundred changes that I have made and I do not know the exact values or lines to change"...truly, if you don't understand what you are changing, and what each line does, you shouldn't be messing with it...and you definitely shouldn't be letting a 3rd party website generate it for you. You're just asking for problems.

Which file are you editing? The one in the "Documents\My Games\Skyrim" I hope?

As long as it's not flagged as read-only, Skyrim will always update Skyrim.ini and SkyrimPrefs.ini whenever it is launched. In most cases, all it does is open/close the file, thereby updating it's "last modified" date. It will reset some values if they're not default, though fShadowDistance is the only one I've seen get reset. Values in Skyrim.ini don't normally get changed by the launcher unless you re-detect your hardware.

Not in my experience, the only time I meet a re-detection is as I explained above when the skyrimpref's line referencing the video card doesn't match what the launcher detects as the current video card.

Excellent advice.

Have you ever used WinMerge for comparing files though instead of NPP?

Yeah, the launcher never changes my custom INI files...not once.

Me to. Except for some reason my iPresentInterval was set to 0 randomly for a little bit, no idea why and my previous backup had it at 1. Crazy stuff.

I've had a similar experience with another command (can't remember which one now) where I was parusing my INI and though "why did I change that to that number...I don't remember changing that at all."

But then again who knows with my lifestyle.

Try leaving your INI open in Notepad++ and launch the game. Afterwards, put focus on Notepad++ and you'll be notified that the file has changed and you'll be prompted to reload it or not. The SkyrimLauncher accesses the INI files, even if it can't/doesn't change their contents. It will change the contents if something is missing, such as your video card designation.

I understand that it access it and changes the last access date as well as anything that is missing...I'm just saying that I've never had the launcher just randomly change things in the file that I had already set to my preferences. There's a difference.

BTW, my files have and will never be flagged as Read Only since that could potentially cause issues if you decide to change something inside the game (via the menu or the console).

EDIT: Just did as you suggested and there were no changes. No need to resave the file. It's exactly the same with the only difference being that the last modified date has changed in xplorer2 but there wasn't any prompt to re-save the file in NPP.

no I haven't but I'll check it out for sure, thx mate

It's a beautiful little (free) program that you can integrated into your Right Click menu so that you can Right Click a file and select Compare To then simply Right Click another file and select Compare. It will highlight specific changes and allows for easy editing. Of course NPP is still great and I can't live without it but ever since finding WinMerge I haven't used anything else for comparing...it also compares entire folders as well.

I never said it randomly changes things. It will change certain values if they differ from the default, one of which is fShadowDistance. That and TreesReceiveShadows are the only ones I've seen get changed and only by the launcher (not TESV.exe). I don't make that many changes to my INI so it is possible that more are likely to get changed in a more heavily tweaked INI. If your video controller is not defined, or if your INI file is missing, the launcher will re-detect your hardware and set the value accordingly. I don't know of any other circumstances under which the launcher will re-detect your hardware and thereby completely replace your INI files.

Fair enough but even those two specific commands that you mention have been custom set in my ini and haven't ever been altered by anything other than me. By all means keep your ini files set as read only if it's not causing you any problem...I'm just saying that I've never had mine as such and I don't have any problems either.