Maybe you created a self-updating, so-called “smart” playlist?
If you used a filter on your library to create this playlist, you usually get a smart playlist. (e.g. “Added within the last x days”, or “unwatched”)
You can discern smart playlists by the small “cog-wheel” icon on their thumbnail picture.
See [HowTo] Create Playlists (Updated for new UI) for an introduction to making playlists, “dumb” and “smart”.
There is a second possibility: if your media files are stored outside the server machine. And you have the checkbox “Empty trash automatically after every scan” enabled, then temporary slowness or connection delays can cause some files to get (temporarily) thrown out of your library. When that happens, they’re also removed from all playlists.
(Settings - Server - Library)
This is usually caused by hard drives, which are spun down to save power, and need too much time to spin back up.
