Does taking a log backup, truncating the log, and then deleting the tlog backup break the LSN chain?
If the avamar tool uses its own tracking method to know what log backup files it can restore, then it will fail.

If it uses SQL internal tables to know what log backup it needs, that is good, but if the file has been deleted, then it will fail.

Either way it will fail since you are deleting the files...so don't :)