I recently came across a compatibility issue with Adobe PDF and SharePoint. No surprise here because Microsoft products aren't even fully compatible with each other, let alone other applications.
The issue: When you open up an editable PDF from a MOSS document
library, make some changes to it, and then want to save it back to the
document library, the default save location is NOT the MOSS document
library.
The easiest solution: Edit the PDF from the SharePoint document
library, provide a link in the PDF that users can copy and then paste
into the file location when they save the PDF. The link should be the
URL for the SharePoint document library. This solution is not the best,
obviously, but it requires the least amount of work, requires no
coding, and gets the job done. Another option is to just not use PDFs.....use Word instead. MS Word can capture SharePoint metadata that can be displayed directly in the SP document library - for both MOSS and SharePoint 2010.
Workaround 1 (only for tech savvy users): You can always map the SharePoint site to one of your network drives. This enables you to actually browse to the document library from the PDF save dialog box.
Workaround 2 (duplicating document approach): Instruct users to save PDF locally, then to upload to the SharePoint site. Then to preferably delete the local copy they saved.
Workaround 3 (find out why this does not work): Create a PDF content type! Creating a content type with a PDF template should allow you to open up PDFs in SharePoint, fill out info, and then save back to SharePoint, right? But wait, this does not work. You get the following error message if you try to open up the PDF content type template from a document library:
This does not work because SharePoint only knows how to open Office file extensions.