I actually have run into the same problem in my Franchise with Albert Pujols. I'm in late September so I'm going to wait and see if the game could read 5 games as 5 days. However, I created another save file and tried this out, and it does work:
Just release the player. You obviously will have to take a cap hit (since I'm so late in mine, I only needed to eat 148k, but it was going to be 2.4 million for the next 9 years.) Then sign him again. His stats will still be slightly decreased like he is on his rehab stint though, and I haven't checked if after 5 games his stats go back to normal.
It could also be beneficial because you can sign him slightly lower than you could be paying him in future years. (aka, with pujols, my salary and cap hit totaled to like 11.7-12/year where i would be paying him 12.6 on his current contract for 2013, not to mention if I get later and his contract goes all the way up to 20/yr.
Hope this helps a little!