In Mass, it is a practical certainty that you will be deemed unsuitable for LTC purposes after being involved in any shooting, justified or not. There are notable exceptions to this, but this is the generally accepted rule.
An FID only allows possession of "non-large capacity rifles, shotguns, and ammunition." So, if you had an FID when your LTC was revoked, then you would only have to surrender your handguns.* Rifles, shotguns and ammunition covered by the FID would not have to be surrendered, according to statute.
That being said, if a crime is being investigated they can and will take firearms and other items related to the crime as evidence.
ETA: *What I should have said here is "...only have to surrender the firearms not covered by the FID." This could include more than just handguns.