We came across an issue where PDF’s with any sort of protection failed to process via ABBYY FineReader Engine 10 SDK. The PDF’s were placed in a network share and then failed to process.
To get around this I implemented a program called Foldermill (Which has a trial to test it with and a very reasonable price for the main product).
The first thing we did was to reprocess the file into a Tiff file, set the DPI and change to Monochrome (As we don’t require colour).
A second job is then setup to convert it back to a PDF file with the PDF/A format. This would pickup files from the first job and then place them into the original share for ABBYY FineReader Engine 10 SDK to then process (Reducing DPI and setting to monochrome means it should be less likely to fail on complex scans).
Both jobs were amended to 60 seconds as we found 1 second would cause failures for those with very slow internet connection when working from home.
We then simply added a new share and removed the old share.