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Hi,
The limit is automatically changed to 1 when indexing file contents. I believe the issue is the large PDF files in size, the server probably cannot handle parsing those and simply fails, returning an error 500 message. For fair use, we recommend a maximum size of 30-60 pages of text at maximum, but it is very highly server dependent. The number of files is not an issue, as the limit is always 1 per iteration.
Higher execution time usually helps, but unfortunately a top time limit is nowadays usually hard-coded into the server, and cannot be increased (especially php-fpm and apache/php, as I found this out recently during testing some things).
There is still one thing you should try, changing the PDF parser method from ‘Auto’ to ‘PDF2Txt’, and if does not work, then try ‘Smalot parser’ as well: https://i.imgur.com/dwkhQdK.png
Usually, the PDF2Txt method is used as a secondary, but it seems faster than the other one (and much less accurate as well). This way, no secondary paring is used, saving some resources, as well as bypassing any possible compatibility issues. There is a small chance that it may go through with either of the parsers selected.