Ye Gods! 3801 relation changes!
How on earth did you manage to check each one? What did you change in each case?
JOSM Validator is your friend. It started with fixing broken polygons (inner way outside mostly), then on initial upload there were several easy to fix validator issues. Just removing the deprecated is_in tags doesn't need to be checked for every object.
Using JOSM Validator on a large swathe of objects without any checking by you counts as an automated edit and should follow the automated edits code of conduct set out at https://wiki.openstreetmap.org/wiki/Automated_Edits_code_of_conduct .
Don't do it, or you'll be prevented from editing OpenStreetMap.
I have regularly seen things that JOSM validator suggested ought to be fixed but in reality were perfectly OK (and to be fair to the JOSM developers they usually fix such issues really quickly when pointed out to them).
Also, changing things so that they are "logically correct" doesn't guarantee that what results actually matches the physical reality. An example of this may be https://www.openstreetmap.org/changeset/71425070 - It looks to me like the "bare_rock" tag ought to apply to the whole area.
Also, for the avoidance of doubt, removing "is_in" adds no value to OSM; it just creates another version of everything.
Back to the original questions "How on earth did you manage to check each one?" and "What did you change in each case?", can you please go through all your changes here and check them, and say what you have changed and why?
I'd start by extracting "before" and "after" relations from your changeset and working out which ones were only an "is_in" change, and then looking at the others to see what happened. That will reduce the relations that you need to look at from 3081 to a more manageable number.
You've mentioned the "inner way outside" ones - those obviously do all need to be checked manually to ensure that you weren't "fixing" essentially "garbage" data.
Andy Townsend, on behalf of OSM's Data Working Group.
You can't make volunteers do work. If you want to ensure that I didn't break anything, that's on you.
Block my account if you want to prevent me from breaking anything in the future. You'll need to find someone else to do this QA work and maintain the administrative boundaries in The Netherlands.
OpenStreetMap is a map of the world, created by people like you and free to use under an open license.
Hosting is supported by UCL, Bytemark Hosting, and other partners.