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Yes this is monochrome CFA

Yes this is monochrome CFA data. So we need to apply the debayer algo on it.
If I do it, one file is well demosaiced, the other not. While as you said, Bayer Pattern is the same.

g_snprintf(fit->row_order, FLEN_VALUE, "%s", "BOTTOM-UP");

This code is for FITS image where data is read bottom up. BUT, that changes anything: one file will be ok (not the same) but the other one not.
The problem is this lack of consistency: this is not normal. Before 0.20 everything was ok.

Debayer ok: https://postimg.cc/0KMm0zVz
Debayer ko: https://postimg.cc/0bv2f6Wh