I want to schedule bulk tasks to run via agents, so I'm running 

create

I see, that makes sense.

specially when dealing with submodules,

BTW: submodule diff should always get stored, can you provide some error logs on fail cases?

Before manually modifying the diff:
If you have local commits (i.e. un-pushed) this might fail the diff apply, in that case you can set the following in your clearml.conf
store_code_diff_from_remote: truehttps://github.com/allegroai/clearml/blob/1f82b0c4010799be6157f5c845c7f6ac48e71c0c/docs/clearml.conf#L157