When you delete a bunch of documents from a database without soft deletion, you select them and press delete. They get a deletion mark and you get a status message that you should press F9. This process of having to press the F9 button to refresh to really delete the documents is already not intuitive for a non-seasoned Notes user.
However, it gets really weird once you press the F9 button. Instead of simply deleting the documents, the Notes client first copies all the documents to some sort of cache. It beats me why. It then asks if you really wish to delete these documents. If you try to delete like 50K documents at once, though, Notes can't fit these documents in the cache, and you get a message that you can't delete more than x number of documents in one go. It gives this message, after it tried to put them into the cache, so after you've already waited for a very long time.
It must be very easy to find out how many documents will be deleted and if this number exceeds the threshold before trying to put these documents into the cache. That's a quick fix. However, why is there a threshold? Why is there this weird cache? Why not simply start deleting these documents straight away like literally every other client?
I think this problem has existed since Notes 1.0 and has never been addressed. My workaround is to create an agent to delete the documents (usually all documents in a view or folder) and run this agent on the server. But that's of course not a workaround that a normal user can do.
I wouldn't change that, it's been like that since the beginning. Deleting is a dangerous thing and it is important that it is confirmed twice and the user can correct the mistake. Moreover, deletion is not a common operation in Notes applications, and certainly not after tens of thousands of documents.
If you need it in some application, write your own LS agent for selected documents. An agent can ask for confirmation at the beginning and will not have this limitation.