The problem is that RSS doesn't really have a concept of "deleted". In general feeds just contain the newest items. Items not on the feed are generally considered old, not deleted.
You can play with heuristics like "This feed is usually sorted by published date and these entries I saw previously should still be here but are missing, maybe they were deleted" but not even have published or updated dates and they aren't always accurate.
This gets even more complicated with WebSub which allows hubs go remove entries they have already seen. So now you need to not do deletion on those requests, and if you turn down your poll rate for feeds with WebSub (which Feedly does IIRC) you might not even fetch the full feed to notice that items are missing for weeks.
The one thing that would actually be reliable here is probably Atom's pagnation and archiving extensions which you can follow to get a view of all of the items in the feed and prune missing ones. However you probably don't want to do this every fetch (otherwise it kinda defeats the point of pagnation). Maybe you could combine this with other heuristics to come up with a decent system. But I'm not even sure these have ordering guarantees so I'm not sure if you are going to fetch potentially unlimited pages just to check if an item was deleted.
If we did want to solve this problem the best option would probably be to add a tombstone element to the feed to explicitly remove items.
TL;DR as far as I am aware neither RSS or Atom have the concept of deletion. Much like sending someone 100 email newsletters unrelated to their subscription will piss them off with no recourse try not to send them 100 feed updates that they don't want.
Edit: It looks like there are tombstone proposals for both RSS and Atom: https://oleb.net/blog/2015/11/rss-feed-item-deletions/. Maybe the author could have tried this, but IDK if anyone supports them.