Final Cut Pro X TM backup issue

To make a long story short, something got messed up with a project and files accidentally got deleted and I can't easily put them back (that's a whole other thing!), but in order to recover, I used Time Machine to go back to a version from a couple of hours earlier. Since I am recovering the whole library bundle, I thought all would be good, but when I checked the recovered bundle, the missing files were still missing! How could this possibly be? Shouldn't the bundle from Time Machine be absolutely compete as it was earlier in the day? Am I missing something very important about how Time Machine backs up a FCPX bundle? Very worrying if what I believe is a safe backup process has a major flaw like this in the way it works with FCPX.