I found this explanation on Cloudy Nights, which seems to be taken from PI forums
http://www.cloudynights.com/topic/492626-pixinsight-updates-broken-bpp-integration/?p=6467668"Here is an explanation for the CFA error I found on the PI forums:
This caused by yourself (or BPP) having set the input hint to 'raw cfa' (which is correct for DSLR).
When the input is in a raw format, PI can find out that it is indeed in CFA format, so it is happy.
When the input is in FITS format, the 'raw' part is ignored (but does not hurt), the 'cfa' part is obeyd (and must be present for some process and do not hurt for others), but PI cannot check that the file was indeed in 'cfa' mode. This information is not in a FITS header. So it tell you: OK, you tell me it is CFA, I believe you, but I cannot check."
I understand this not something I should worry about ?