Smile has updated both PDFpen and PDFpenPro to version 5.8.5 to add compatibility with OS X 10.8 Mountain Lion. Additionally, both releases fix an issue with scanning when running 10.7 Lion, as well as an issue where resampling at a lower resolution produced a larger saved file. Both updates are rounded out by other unnamed minor fixes and improvements. ($59.95/$99.95 new with a 20-percent discount for TidBITS members, free update, 40.7/41 MB)
Extract Directly from Time Machine
Normally you use Time Machine to restore lost data in a file like this: within the Time Machine interface, you go back to the time the file was not yet messed up, and you restore it to replace the file you have now.
You can also elect to keep both, but the restored file takes the name and place of the current one. So, if you have made changes since the backup took place that you would like to keep, they are lost, or you have to mess around a bit to merge changes, rename files, and trash the unwanted one.
As an alternative, you can browse the Time Machine backup volume directly in the Finder like any normal disk, navigate through the chronological backup hierarchy, and find the file which contains the lost content.
Once you've found it, you can open it and the current version of the file side-by-side, and copy information from Time Machine's version of the file into the current one, without losing any content you put in it since the backup was made.