Basically I am wondering if deleting references in game can cause any problems, as these deltions get stored in my save game. And following on from that I would like to know if there is any editor for Oblivion saves?
The reason I am wondering is that a few weeks ago I encountered the issue where Oblivion would CTD when trying to load any saves, even if these saves had been loading fine before (one of them I must have loaded twenty times trying to chase down a bug). Starting a new game and loading saves from that new game was no problem. In the end I got the saves going again but only if I removed a few mods, especially Better Cities and Unique Landscapes. This seemed strange, as that very load order had been playing fine for a long time, new games with the same load order had no issues, and clearly if something had gone wrong with either BC or UL this would have bene flagged up quickly in the respective threads. Even doing a proper clean save would not allow me to add BC and UL back in. Happy to at least have gotten my 400+ hour working again, I reluctantly decided to continue playing without BC and UL, and I have not encountered any further problems. Yesterday I needed to get into the Newlands Lodge in Cheydinhal and could not activate the door, which is when I remembered that - probably due to me not having fully cleaned a mod, having the wrong compatibility patch or simply not having made a proper clean save when updating - at some point some doors in Cheydinhal had become doubled and I had used the console to disable the doubles, which in this case turns out to have been the original Oblivion reference.
This got me wondering whether this is actually the cause of the CTDs when trying to load saves. If I understand it correctly, a savegame can be considered as basically a mod which loads last, and deleting references in mods is bad as it causes problems if another mod tries to use the now deleted reference. Since the save always loads last this should not be an issue, but I recently read that some mods use scripts to reposition objects, usually to ensure compatibility with other mods. Presumably these scripts only run after the save has been loaded, so what would happen if a script tried to move an object which I have already deleted in my save?
Additionally, while returning the doors or other easily noticeble deleted objects is easy enough (although having to find the reference ID in the CS is tedious), it would be easier if there was a save game editor that would allow something similar to the 'undelete deleted reference' command from TES4Edit. Indeed, if deleted references in a save game really do cause problems, such an editor would be a very welcome help, as I can no longer remember which doors/rocks/etc I deleted during my game. So, does an editor for save games exists?
I would really appreciate if someone knowledgeable about these things could comment/advise. Many Thanks!

You appear to be under a misaprehension. Disabled refs are not deleted, just diabled. We disable refs are the time to replace them, or more accurately we usually undelete them in TES4Edit.

Having said that, you might be right. about the cause of your CTD's. Over the weekend I had a persistant CTD which I just could not chase down, even removing the mod that I thought was the problem (something I am working on) didn't fix it. In my case the game would CTD on load of a save if I had the BASH Patch loaded, otherwise it was fine. Eventually, I did get it working, but only after doing a double clean save, disabling the mod, loading, saving, re-enabling the mod, loading, saving - loading BASH Patch.

Very stange, and frustrating because I only loaded that save by accident as I had given up on it - so I don't actually know what I did.

That would make sense, but now I am wondering whether I also used something like "setdelete to 1" - it was a long time ago, and I may be (mis)remembering Morrowind console commands.
Anyway, I might try loading a save with BC and UL but without the Bashed Patch (although it may prove difficult as some mods need it). Thanks for the advice!

You must be thinking of morrowind, these are the commands for Oblivion's console: http://www.uesp.net/wiki/Oblivion:Console

You should be able to load the game without the Bash Patch, the only issue is that some of your mods will not be merged, patches may not show etc. It doesn't appear to cause any major chaos though. Try loading and saving without it and without the problem mods.

You might want to offer a prayer to any deity of your preference as well.

Prayer answered.... oh wait.

Try this in the console:

prid 31BA1
enable

That should bring the missing door back to life.

Many Thanks, I already got that door (and a few others) back - hope you did not wade through the CS just on my behalf.
In any case, I was more worried about the less noticeable objects I may have deleted (eg, rocks that may have covered cave entrances, floating plants) and what effect these deletions may have in-game. But if "setdelete" is indeed a Morrowind-only command then I can only have disabled objects so that should be fine.
I am, however, considering making some (non-human) sacrifice to ward of any evil that may come from loading a save without a Bashed Patch!

EDIT: Wow, Thank you so much Sigurd Stormhand, doing a clean save of the Bashed Patch worked! Bizarre, as I had of course rebuilt my Patch after any changes to the Load Order. But it worked, so I am just grateful for that!