Fallout – How does Fallout handle modded savegames after removing the mod

Concerning the TR_XXX.esm, you're most likely trying to use Tamriel Rebuilt (good choice!) Antediluvian Secrets, which requires Map 1 (Telvannis) as well, so I guess the latter has been forgotten.

Concerning the warning, this means that one of the plugins you are using was saved using a different version of the game main files, e.g. native Morrowind.esm while you're using the Morrowind Patch Project. You can usually ignore this, although you should at least once check whether you're accidentally using a Morrowind-without-Bloodmoon version of a plugin that also has a Morrowind-with-Bloodmoon version if you have Bloodmoon installed or vice vers.

If you want to get rid of the warning for good, you have to open the respective plugin's .esp file with the TES Construction Set (using your actual Morrowind.esm etc versions as base files) and simply save it again (keep a backup though). That should update the claimed dependency without modifying anything else.

You can actually rename the FOSE or FOMM launchers to 'FalloutLauncher.exe', which is the executable Steam looks for when launching the game. Steam will then launch the appropriate program, but still think that it is Fallout.

For example, I did these steps with FOSE:

• Navigate to Fallout 3/New Vegas's folder under steamapps.
• Change the FalloutLauncher.exe file to be a different name, such as FalloutLauncher-orig.exe (in case you want to revert).
• Create a copy of the fose-loader.exe file, and rename it to FalloutLauncher.exe (Leave the original named as fose_loader.exe, as FOMM will look for this file when you launch FOSE through it.)
• Click Play in Steam. It should launch the game with FOSE.

I chose to do this with FOSE instead of FOMM, because FOSE launches the game directly. If I want to access FOMM, I still have it's link as a 'Non-Steam game'.