I do not recall the count in the CCD module and assumed it was okay.
The flats were all taken in the end and the 0/0 remained.
I thought the process halted when monitoring the Setup Module Summary. The CCD module was working, and next set of flat I can confirm.
I think I had something similar with light frames as well recently where the first frame was being overwritten due to the counter not incrementing. When I added time stamp to the file name I could get all the frames but they are all numbered 001 like this:
Light_OIII_0.500_secs_2017-05-17T00-24-54_001.fits
Light_OIII_0.500_secs_2017-05-17T00-25-08_001.fits
Light_OIII_0.500_secs_2017-05-17T00-25-22_001.fits
Ok I spent most of the days fixing some issues related to counters and also filenames. Well, it _seems_ all conditions are working. It's getting quite complex with local vs remote vs dynamic plus all the flat calibration stages. At any rate, now timestamp is also supported in the remote files names the same way they are supported on local files. Personally, I never used TS in my filenames, everything should be pretty well organized as is now and this information is already stored within the FITS header, but it is there anyway.
Please check the next PPA update, hopefully I didn't break more things.
The following user(s) said Thank You: nMAC, Stephen, Jim