Blackout and now "No such file or directory"

Before posting this I’ve read through a few handful posts where a similar errors have happened.
Basically I had a blackout and Yunohost Pi Server went offline.
After rebooting everything seemed fine, any domain on the “nohost.me” worked fine alongside their apps. Later in the day I wanted to access my nextcloud and saw “403 Forbidden”, began checking other apps under the domain I used and all of them didn’t work. I tried other solutions checking file admins, etc, and it resolved some stuff but I’m currently stuck at the following issue.

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/moulinette/interfaces/api.py", line 494, in process
    ret = self.actionsmap.process(arguments, timeout=30, route=_route)
  File "/usr/lib/python3/dist-packages/moulinette/actionsmap.py", line 599, in process
    return func(**arguments)
  File "/usr/lib/moulinette/yunohost/log.py", line 419, in func_wrapper
    result = func(*args, **kwargs)
  File "/usr/lib/moulinette/yunohost/domain.py", line 190, in domain_add
    _certificate_install_selfsigned([domain], True)
  File "/usr/lib/moulinette/yunohost/certificate.py", line 173, in _certificate_install_selfsigned
    with open(conf_file, "w") as f, open(conf_template, "r") as template:
FileNotFoundError: [Errno 2] No such file or directory: '/usr/share/yunohost/yunohost-config/ssl/yunoCA/openssl.cnf'

I tried a new domain and that didn’t work, can’t renew certificates, I saw another post who had something similar happen to them but they were missing other directories. I was missing a few of those to, but honestly I don’t know what happened?? Certain apps say they simply can’t run and I’m not sure why. Like my calibre library says this error.

-- Logs begin at Mon 2022-10-24 12:52:58 PDT, end at Sun 2022-10-30 18:20:55 PDT. --
Oct 24 12:53:04 systemd[1]: Started calibreweb.
Oct 24 12:53:04 systemd[657]: calibreweb.service: Changing to the requested working directory failed: Permission denied
Oct 24 12:53:04 systemd[657]: calibreweb.service: Failed at step CHDIR spawning /bin/sh: Permission denied
Oct 24 12:53:04 systemd[1]: calibreweb.service: Main process exited, code=exited, status=200/CHDIR
Oct 24 12:53:04 systemd[1]: calibreweb.service: Failed with result 'exit-code'.
Oct 30 18:20:55 systemd[1]: Started calibreweb.
Oct 30 18:20:55 systemd[4350]: calibreweb.service: Changing to the requested working directory failed: Permission denied
Oct 30 18:20:55 systemd[4350]: calibreweb.service: Failed at step CHDIR spawning /bin/sh: Permission denied
Oct 30 18:20:55 systemd[1]: calibreweb.service: Main process exited, code=exited, status=200/CHDIR
Oct 30 18:20:55 systemd[1]: calibreweb.service: Failed with result 'exit-code'.

I think my server is just fully corrupt, is there a way to repair these issues? Like a rebuild YunoHost?

My YunoHost server

Raspberry Pi 4 8GB
YunoHost Version 4.4.2.14 (stable).
I have access to my server via web admin and through the Screen as well. Just seems to be stuck in this broken state, can’t add, remove, edit, or use anything on it. Only apps installed on NoHost.me work, but can’t update SSL or change domains for them.

Thank you, any help or suggestions appreciated.

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