I think 0.139 used CHD v4 (lr-mame2010) and 0.161 used CHD v5. You'll need a rollback file and use chdman from a command line (this can take a while for a whole set) if you can't find v4 CHDs.
I think these are the correct CHD versions if not they are close.
mame4all-pi (0.37b5) - N/A (CHD wasn't introduced until 0.62 or 0.63)
lr-imame4all (0.37b5) - N/A (CHD wasn't introduced until 0.62 or 0.63)
lr-mame2003 (0.78) - CHD v3
lr-mame2010 (0.139) - CHD v4
advmame-.94 (0.94) - CHD v3
advmame-1.4 (0.106) - CHD v3
pifba (0.114) - CHD v3
lr-fba (0.154) - CHD v5
lr-fba-next (0.173) - CHD v5
gngeopi (0.138) - CHD v4
Knowing the CHD versions could be useful as the Pi gets more powerful. :) I think some versions of MAME could use earlier versions of CHDs as "readonly" but if it was a CHD that could be written to for like high scores or something it doesn't work without the correct version.
Instead of modifying the CHD directly (which would change the internal/external hash--MAME only cares about the internal hash which is data minus metadata) I believe MAME would auto-create a <game>.diff file and use it.
I think current versions of chdman can verify older versions but not vice versa for obvious reasons. :)
Newer versions command line:
chdman verify -i area51.chd
chdman info -i area51.chd (shows CHD version & other info)
Older versions command line:
chdman -verify area51.chd
chdman -info area51.chd (shows CHD version & other info)