So far, we've been running JIRA on http. In version 8.4.0 we switched to https and configured JIRA accordingly.
After update to version 8.4.1 we had to re-import the certificate and set the base URL back to https. Do we have to manually switch from http to https after each update? After the update only a connection with JIRA was possible via http.
Yes. The installer can't know what you have configured in order to enable https, so it just installs a standard set of files as though it were an ordinary http install. You need to re-do any non-standard configs (such as https) after an upgrade.
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