Hi Roman,
using the batchrun (selecting more than one datfile at a time) there is a small issue.
I have a few datfiles previously scanned, all of them are green (full set of roms available); when I use a batch run on them, selecting the "Rebuilder run only", after the run all datfiles are grey, as if they where never scanned before.
This does not happen if some datfiles are green and some are red.

---------EDIT----------

Made some more testing, the problem is NOT related to the status of the datfile (red,green), it's related to the version of clrmame used the get the status!!
Datfiles whose status was set with a previous version of clrmame loose their status during batchrun with "rebuilder run only" activated; datfiles whose status was set with the same version of clrmame keep it after batchrun.

I do not know if it's an issue or if it was intentionally coded this way.

All the best