Normally for the build in database you would only need to copy the deployment/data directory. Check your data directory if it contains a hsqldb directory and check the size of default.script file. And may be you should switch to postgres. It's free and you would not have lost your data because it is on a seperate location.
Just ran another test, and apparently after replacing the data folder, you probably need to re-deploy (I say probably because I was having other issues and I had to restart the server I am working on). After doing this, I was able to see my data again. Hope this helps someone else in the future.
Again, many thanks for all the help!