missing stacks after portainer "crash"

[canajien]

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After some recent updates I have managed to lose some of the dockers portainer was managing.

I recently updated portainer then docker on ubuntu server 24.04. I updated portainer first, made sure it still worked then updated the docker.

Before the crash I was only running 3 services, vaultwarden, immich and stirling pdf.

After updating docker only vaultwarden still works.

Portainer was broken and would not run, kept restarting itself so I did a clean install, removed the data folder and its working again.

When I run docker ps -a it tells me portainer and immich are running along with valkey

When I look at the web ui for portainer it confirms immich and valkey are there.

Stirling pdf has gone missing, entirely.

Immich does not connect either through the client or the browser.

And vaultwarden is nowhere to be seen in portainer or the docker command line. but it is running just fine, I can access through the browser and android client along with browser add-ons.

It's the last one that concerns me. I have backed up my passwords and am wondering what to do?

Is there anyway I can get docker and therefore portainer to talk to it again, or should I opt for a clean wipe of everything and start over?

What's the best way to prevent this in the future?

Thanks in advance for your suggestions and insight.