In theory, you could write your own migration file (Just stick it in the game's migration folder, with a unique name. The game records what scripts have been run so they only run once)
You'll want to use the json version of the migration, because that loads when you load the save game, and convert all of entity 1, into entity 2.
write the script, and have it convert all of the ones from the mod, into ones from the base game, or another mod.
The only issue with this is, Positions are only retained if they've been changed (Like, if you use Bob's Inserters to change positions, those are saved as extra information in the entity, and if you change the entity via the mentioned method, the extra information is copied onto it, so the new positions are retained). If you replace a long handed inserter with a normal inserter, then the pick up and drop positions will change to that of the new inserter.