I don't think so. Unless I'm mistaken, recent/missed calls are not backed up. Just settings and actual content. When you completely wipe and factory restore the phone, the file system should be repaired and that database should have the proper permissions. I'm fairly confident it would be fine, but if you want to make sure just do this:
1. Wipe the phone. Complete factory reset, get rid of everything.
2. Afterwards, set it up as your phone again but do not sync. Basically, get it to where it has your phone number affiliated and can make calls, but that's it.
3. Call a few random numbers and just hang up right after you call. See if they're in recent calls.
If you do this and it works fine, go ahead and sync all your stuff back. It should still work. If it doesn't, at least we know it IS the backup that's corrupted. But like I said, the root filesystem of the phone should not be in the backup, just content to populate the device.