I have the same problem however the fix did not quite work for me.

I have two FreeIPA servers running as a replica set, both running Fedora 40. I 
updated one to Fedora 41 and the ipa service would fail to start. Digging 
deeper I could see that when the service starts it tries to perform an upgrade. 
One error message said to look at /var/log/ipaupgrade.log. In this log I could 
see errors relating to failing to authenticate with the CA REST API.

I tried Vicente Quintans fix above by replacing all occurrences of “/rest” to 
“/v1” in /usr/lib/python3.13/site-packages/ipaserver/plugins/dogtag.py. This 
did fix some stuff as I could then start the ipa service which implies the 
upgrade part is now working. I can also sign into the web UI. The problem I see 
is that when I go to the authentication page in the web UI I get a popup error 
saying:
IPA ERROR 4301: CertificateOperationError
Certificate operation cannot be completed: Unable to communicate with he CMS 
(Failed to parse error response).

Because these are production servers I have rolled back. Problem is that Fedora 
40 is end of life very soon.
I’ve kept the broken machine, plus I can easily replicate the error if need be.
Not sure what to do next.
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