Did your container have host volumes for /config and /cache? It sounds like when we pruned docker it purged all your Jellyfin data. Which would only happen if you did not provide permanent storage for /config.
Jellyfin 10.10.7 (Docker)
Ubuntu 24.04.2 LTS w/HWE
Intel i3 12100
Intel Arc A380
OS drive - SK Hynix P41 1TB
Storage
4x WD Red Pro 6TB CMR in RAIDZ1