Sorry I missed this. Whenever there is a mismatch between the tool and the site, you typically just need to update recruits in the tool. For OOV cases, often what happens is you run the tool during the previous season then forget to run it again when the new season rolls over (when all the scores go back to 0-0). When that rollover happens, your team's vision changes, and if it went up, there will be guys in the tool marked OOV that are actually now in your vision. I've never actually seen a case where there was a mismatch and updating recruits didn't get things synced up properly.
As a general rule of thumb, you should update recruits every time you're about to do recruiting. You should also be aware of when each recruiting cycle ends so that you don't run the update in middle of a cycle change or update it on one cycle and then do recruiting on the next. If you follow that, you should never run into out-of-sync issues.