Hi Remco,
thanks for the support.
I also created a small standalone proof-of-concept, and it indeed seemed to be working.
So I updated our current solution to Slowcheetah v2.5.10.3, and it was still not working. Then I noticed 2 things:
Now, everything seems to be running smoothly again. (after rechecking if the "Additional files to include" pointed to the correct directory)
So sorry to have bothered you, it was not a NCrunch issue, but a SlowCheetah/Nuget issue.
Thanks for the help!