That should not be happening. I would suggest possibly that you do a "Check Return" for the client before ending the day. That might help lock the data in. 

Personally I would never attempt to enter that many transactions in ProConnect. I would enter only one item for all short term where basis is reported. One for all long term where basis is reported and probably a "see attached" for short term basis not reported and another "see attached" for long term not reported.