That should work. Most of the stuff should be handled by ownCloud through its own .htaccess file.
I don’t have a debian machine to check, but if the problem happens only with debian (at least so far) maybe someone could upload the virtual host configuration to have a look at it.
I have been running my ownCloud on Apache on Debian Stable installed from the official ownCloud .deb package for approximately a decade. With one exception quite some years ago. I have been upgrading the same installation (and the operating system) in place. I experienced no disruptions during this recent upgrade. I don’t share this to discount the experience of others in this topic, but rather to offer my installation as a reference for comparison if it would help.
Our installation is among those that tripped over this recent install AND that is once again running after reverting to .htaccess from 10.11. It really does seem that a better check needs to be part of the upgrade.
I’m still not 100% sure how this issue is caused (how to reproduce it), but perhaps it has something to do with rewrite base or subfolder installations:
However there is an occ command to update the .htaccess file. Perhaps that would regenerate the correct one for installations in subfolders / using (or not) a rewrite base:
Perhaps that would be worth a shot for people experiencing the issue? Please take another backup of the .htaccess before running the command, and be prepared that in a fixed installation, it might undo the fix.
In previous core versions the rewrite base config.php option was not added to the generated .htaccess file. The use of a more hardened .htaccess file in version 10.12.0 (being introduced by tweak rewrite conditions in htaccess by C0rby · Pull Request #40584 · owncloud/core · GitHub) caused the files view in the web UI to be empty in URL via subfolder plus index.php-less setups. Additionally, the desktop app was not be able to sync and an error 405 (Method not allowed) was returned. Rewrite base is now correctly added to the .htaccess file.