Some observations:
Strangely enough even newly added courses can have "changed" skills, they are being kind of "skipped" putting my progress further down the path, even though I only did one test lesson in the very first skill and I never went deeper down.
I initially had it in multiple newly added courses but these "changed" labels are gone now - I didn't do anything at all to make it happen, I just reloaded the data a few days later, so it appears that duolingo data is changing without any effort on our part and all those errors could be cleared one day - in theory.
If changed skills are there, but there are no normal/finished (non-grey) skills after them, such skills can be cleared by gradually doing your lessons as usual - through and past all the units containing the affected skills.
If changed skills appear before any normal/finished skill, they cannot be cleared - I tried doing the affected skills in both practice (+5xp) and legendary modes, I tried doing the entire skill (unit), I also tried doing the entire next unit on the path, but none of this would help.
So I went on to reset the course and:
- yes, resetting the course clears "changed" skills
- xp points are substracted from the total upon deletion of the course, word count is reduced as well (understandably)
- "learned_ts" timestamps are gone, they're not even there in duolingo data anymore, so new dates will not be assigned
be updated unless you're brave enough to reset your course... 
