Not surprising. The new Podcasts app deleted years of downloaded podcasts when I updated, including a lot that are no longer hosted on the web. For some reason the "sensible default" in the new app is to delete anything beyond the most recent ten episodes. Now I need to remember to restore from backup before it gets overwritten, heh.
> For some reason Giving you the other side of this: Podcasts was essentially a disk-space-leak made app, if you subscribed to any podcasts that you never actually listened to (but still listened to others, and therefore regularly opened the app.) It would just pile up new unplayed episodes forever, eventually taking up tens of GBs of space, on a device that doesn't have all that much space to spare.
For example, Apple themselves have a stack of playlists for different genres that are updated on a weekly basis, so after a few months you end up with a ton of downloaded files for songs that are no longer in your library (because they've been rotated out of the playlists).
Problem is, because they're not in your library there's nothing surfaced in the UI, so there's actually no way to know that it doesn't clean up after itself until you go to investigate why you have no disk space.
No idea if this behaviour has survived the transition to Music.app, but considering it seems to just be iTunes with a fresh coat of paint, it wouldn't surprise me.