[whpalmer4]

Most likely, you've only linked to the documents, not actually embedded them. Here's how to check:

Use the Windows->Attachments List command to bring up a window showing all of the attachments in your database. Do the PDF files appear there? If not, they won't appear on the iPad, either.

When you attach files to an action or project, if you do it by dragging, you need to hold down the option key if you want the file embedded (the cursor will turn into a green circle with a white + in it). If you attach by using Edit->Attach File... there is a radio button to control whether you embed or link.

A related bit of advice: too many embedded file attachments will make sync go slower, so when you no longer need those attachments, weed them out. The Attachment List window is handy for this; clicking on the column headers will allow you to sort the display, and double-clicking on an item will take you to it (except in the cases where a questionable implementation decision gets in the way — if you can't seem to find the target, change your view to the All Items perspective, go back to the Attachments Window and try again).