I've cleaned mods before and I use Miax's manual (but that doesn't mean I didn't make a stupid mistake). Here's what I've done and what resulted:

• Did not clean FWE, MMM, WMK, any of their optional plugins or any of the FOIP patches.
  
• Cleaned pretty much everything else on the list.
  
• Crash on startup.
  
• Disabled all mods, game runs fine.
  
• Enabled FWE, MMM, WMK, Project Beauty, and FOIP. Game runs fine.
  
• Enabled A Decent House. Crash on startup.
  
• Restored A Decent House backup ESP. Game runs fine.
  
• Enabled all mods. Crast on startup.

So, before I keep going, enabling mods one-by-one and finding that I need to restore the backups, I'm looking for some input.

What could have gone wrong? Are there common mistakes I could have made?
Can regular, non-mistake-making cleaning ever cause crash-on-start? If so, how exactly?

Thanks,

gothemasticator

Sometimes FO3Edit misreads NAVM's as 'dirty' when they're not, and it will remove them while 'cleaning', leaving navmeshes and/or NAVI without what they expect to find. It only happens if the sole difference between two compared versions of the NAVM(s) are identical other than their external connections (NVEX) subrecord data, making it look like this in FO3Edit. To avoid this, tick the NAVM's NavMesh Generation - Ground box in FO3Edit and it will read as an override so it won't be removed inadvertently.

Alternatively, you could just not 'clean' the cell and worldspace groups as those are the only ones that will ever have NAVM's. To get around the crash, you can remove NAVI, but at that point it's probably better to revert to an unaltered plugin.

FOOK2 v1.1's files, btw, can be cleaned and nothing will happen.

Thanks for the education! Yeah, I reverted to the backups. I'll just start the cleaning process again and look out for NAVMs.

gothemasticator

Glad to share. If, after everything's filtered, a NAVM looks like this, it's safe to delete, but afterward you have to open and save the plugin in the GECK to rebuild that Navigational Mesh Info Map (NAVI) record.

If I remember right, Miax's manual recommends everyone to clean their own mods before upload but advises against cleaning other people's mods.

Not exactly correct.

Yes, the manual is part of the experienced modders' attempt to encourage mod creators to clean their mods as part of production. It's good practice and it avoids problems for mod users, including some crashes.

No, there's no advice against cleaning others' mods. In fact, it's necessary for many mods. Either the authors don't know to do it themselves, or they are no longer updating the mod - in which case it would never get cleaned.

gothemasticator