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Hi @kapdome, and welcome to the LE community forum
This can cause problems when not configured correctly.
I don't use CF, so I can't advise you on that; But it needs to allow the challenge requests to reach your server.
I have no idea why anyone would use this software.
I like nginx, but NPM is useless and causes more trouble than it solves.
Troubleshooting advice:
check your nginx logs and see if the challenge requests make it to your server.
If yes, then NPM (or the nginx config) may be to blame.
Note: CF will redirect HTTP to HTTPS [which may be unexpected by your system/ACME client].
If no, then CF is to blame, and it needs to be set correctly.