I've been using clrmame with every new mame release to
update my roms with the following procedure:

I keep all the existing roms in a single directory, say
mame089, and all of the new roms in various directories like
89u1, 89u2, etc.

Instead of rebuilding all of the roms, I just put the
directories with the new roms in the Add files path and
then have clrmamepro scan the roms and fix them.

Is this the most efficient method?

It seems to take a long time to fix a rom that is fairly
large.

Is ClrMamePro recompressing the files? Could it be
more efficient if it didn't recompress the already
compressed data? (that is just copy the compressed
data from zip to zip)

BTW thanks for a great tool in ClrMamePro