Instead of trying to batch capture

Instead of trying to batch capture the entire master clip, try batch capturing just the sequence with handles. The re-capture any additional footage you need from the original tape and edit away. To fix what you've done you may need to go back to the attic to retrieve an older version of the project.The DSR11 was not a frame accurate editing VTR so it is not that surprising, although if you had handles on the original batch capture of the master clip that would explain your original error.You can't muck around with master clips that are linked to sub-clips as you've discovered.