GD-ROMs are a subset of the CD-ROM issue; some of them also were old-format CHTR metadata and the upgrade on the metadata changes the SHA1 (but not the "Data SHA1", indicating no changes or damage to the actual data). GD-ROMs created with 2009 or later versions of chdman (such as initdv3e which I just added in u1) will update to v5 with no SHA1 changes at all.
So the source needs to be updated to the new SHA1s where applicable for these GD-ROMs, but no further action needs to be taken. (As opposed to CD-ROMs where the source should be updated *and* those sets should be marked BAD_DUMP).