Thank you very much for the details, it helps a lot.
I logged in, and checked the index table panel and re-created the index table. It all went down without errors. The indexing process can be very processor heavy especially for PDF documents, so the server may have throttled the processes and reported the error. It seems to be all right now.
Oh sorry I should have told you. I gave up and set it for PDF2text and then it sort of worked, although it misses lots of search terms.
But if you set the indexing to the first choice (smalot parser) then you get this 500 error very consistently.
It says “initializing please wait” for maybe 60 seconds and then it displays the 500 error. You can look now to see it.
The Smalot parser (default) requires php-xml and ZipArchive to be enabled. If I had to guess, then php-xml may not be installed on your server. Here is the recommendation from the official WordPress site for which modules should be installed.
Try checking those if you can, and once the recommended one are installed, I am almost certain that the “Auto” option with the PDF parser will work, and get more words out of the files.