My advise is not to mix mame and fbneo roms just keep them in separate folders.
Otherwise you can't keep track of which is which.
About new roms and emulator releases.
I would not spend hours and hours finding which rom still works and which needs updating if not necessary.
I would just backup all and get all new ones and filter them again which is much faster.
For lr-fbneo this would be easy as I explained.
For lr-mame2003plus I don't know.
I could be wrong but for lr-mame2003plus I don't expect many updates.
I never used CLRmamepro so I can't help you with that.