Hi Vermin96,
As we understand it you're no longer able to search for old messages in Spotlight, is that correct?
Immediately after an update Spotlight will re-index itself, a process that can take several days depending on the amount of data on your Mac.
Additionally, once a message is deleted, a copy of it may be saved in the temporary files on your Mac, and as such searchable via Spotlight. That being said, the expectation is once a message is deleted, it is not recoverable short of restoring from a pre-existing backup.
If you believe there is still information missing from the Spotlight search results that should be there, we'd recommend rebuilding the Spotlight index. The steps to do so can be found below, however in general deleted messages are not expected to show in Spotlight results.
If you have further questions, feel free to reply to this post.
Cheers!