If you absolutely must use a specific mod that is no longer being updated and requires the .esm file, you can download FCOM version 2.82 from the "Old Files" section on Nexus. This version still uses the fcom.esm format.
The most reliable fix is to download updated versions of your patches. For example, if you are using Militarized Minutemen , ensure you are using the compatibility patch found on the FCOM Nexus Mods page rather than older standalone patches that may still be looking for the .esm version. fcom.esm missing