I got into trouble with pdf files directly saved out of Microsoft Word. After doing some changes and trying to save the file it gets broken. The solution was to only take pdf's saved as PDF/a. Is there any possibility to support pdf files which are not PDF/a?
May you provide more details about the issue you are experiencing?
Please, send us one of your original PDF files, the output after modifications.
Give us a reproducible sequence of modifications which is altering file structure.