Personally what I might do is make each batch script create a lock file after first checking for the existence of the other script's lock file and exiting if it is found. Or you could make it wait in a loop until the other script's lock file becomes non-existent. If it is not found, then the script creates its own lock file, performs it operations, then finally deletes its lock file.
e.g.
REM Batch A
if exist batchB.lock exit
echo abcde > batchA.lock
bla bla
bla bla
bla bla
del batchA.lock
REM Batch B
if exist batchA.lock exit
echo abcde > batchB.lock
bla bla
bla bla
bla bla
del batchB.lock