ApexSQL Data Diff
“Check-in failed Source control error: Cannot checkin pending changes” error can be encountered during the synchronization to the Team Foundation Server repository, when the synchronization script exceeds 300 MB in size This error can be also encountered if the connection speed between local machine and Team Foundation Server hosting service is slow.
Restart the application and choose the same data sources
After setting up the data sources, click the Compare button in the New project window
Check only a few object in the Results grid for the synchronization process. Note that synchronization script for those objects/rows shouldn’t exceed 300 MB in size
Click the Synchronize button from the Home tab
Select the Update files to source control action in the Output options step of the Synchronization wizard
Click the Synchronize button in the bottom-right corner, of the last step in the Synchronization wizard
ApexSQL Data Diff 2016.03.0110
The issue is scheduled for resolution in the next release of ApexSQL Data Diff 2017, planned for the Q4 2016.