"I open my file and there are only a couple items present."
Sorry to hear you are having trouble.
We're pretty confident that all your data is still intact. Paperless stores data in Library files. You can have as many of them as you'd like. Often times people use the default name and place to store their Library file (this differs if you bought from the Mac App Store), which is, the documents folder, with a name of "Paperless Library.paperless". Typically when someone thinks they've lost all their info and curses our existence, it's just that they've opened a different library or they didn't transfer their library from another drive or computer when doing an OS or hardware upgrade.
We recommend searching your drive and see if there isn't a Paperless Library.paperless that contains all your files. In addition, you can find the location of your current library - by command clicking on the title bar of the library window - right on the name. That shows you the path to that file. You can also look at the size of the file. We've seen times where a person thought they'd lost all their documents but they had performed a search and filtered all the results so only a few documents were showing. The file size of the library might be a good indicator of the amount of data it contains. if it's only few Megabytes then it's likely not your main library file.