Although I haven't seen this problem personally, I've seen quite a few reports in my mod section of my mod being Redded out. After further investigation it was caused by a Base mod >= 0.12.0 check fail, due to base mod not being loaded, or checked properly.
Details in my forum. https://forums.factorio.com/forum/vie ... 436#p98085
[0.12.2] Base mod disabled
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bobingabout
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Re: [0.12.2] Base mod disabled
I guess, that it might be possible result of other bug I just fixed:
If that is the case, it is fixed for the next release.
It theoretically could happen, that as the mod is not loaded, the other mod that has it in it's pre-requisition might not load as well and disable itself.Fixed that non-default mods were not loaded during the first start of Factorio after mod-list.json was deleted.
If that is the case, it is fixed for the next release.