I have recently swapped my server certificate, which I have created myself. But then, my Android client immediately compained about the certificate and didn’t let me connect. I did not see any way to accept the new certificate. Now, several hours later, the app suddenly asked and let me accept the certificate. But it would be imho much better to have an option to just “randomly” accept a certificate, so that there’s no interruption in the synchronisation.
feature (or bug) requests are raised best via the issue tracker since that way you’ll be reaching all the Android files app developers. https://github.com/nextcloud/android/issues/new/choose
A new certificate is provided by a web server once it has been restarted or forced to reload its configuration, that’s usually not a Nextcloud issue.
On the client site it is usually requested/verified when establishing a new connection to the server. So you have to make sure that the app is definitely stopped from running in the background before you’re establising a new connection.