Fix a pdf scrapping payment receipts web based system

I have a customer (school) that has an extranet where employees (teachers mostly) see their salaries deductions online. The system was working fine until one day, we discovered that, for some reason, the scrapping was not storing the receipts accordingly for each employee.

Current system does the following:
1) HR employee uploads a couple of PDF files monthly (each PDF contains multiple receipts).
2) System splits the original PDF files.
3) System scraps each new PDF file and gets username and some other data. <-- NOT WORKING
4) System inserts records in a table in mysql db to relate which user has which receipt
5) HR employee downloads all the new PDF files
6) HR employee digitally signs the new PDF files
7) HR employee uploads new PDF files and overwrites the non signed ones.

HR employee repeats this same process monthly.