You could try to sync without the TPS set as a quick fix, but I think i'd step back to the point where you close the bleeds. Just keep track of how much they turn to closed. You can go back to the same setting when done and see how it idles. Air bleeds are set for CO and idle speed, not balance. Also, they are out of the picture after a certain throttle angle, so honestly it may not matter much, I'd still close them first though. With luck, you'd be restoring the set up to where it was last time the full baseline adjustment was completed. If it doesn't idle well after, or feels off at cruise with the throttle just cracked, you'll need to go deeper.
When setting TB balance, remember that throttle angle under load for a given RPM is not going to be the same as the throttle angle with no load revving in your garage... You're syncing for throttle angle, not RPM. If you are having issues with vibration at say, 5K under load, you'll want to set balance to maybe 6 or 6.5K with no load. To see the RPM you want to get closest sync, ride the bike on level ground with the vibration. Note the RPM. Without letting off the throttle, pull in the clutch and let the engine rev. That no load RPM is where your throttle angle is going to be best synced when you get it in your garage.