Yes, you can delete the subtask step(s) for specific client(s) if the form/task has been set-up with User Defined Subtasks. To delete, click on the record selector (area at beginning of step) and then hit the delete key on your keyboard. 
TIP! When crafting a subtask type, consider setting up more steps than might be needed for all clients and then delete the unneeded steps on the client task/form level where they don’t apply. This approach is simpler, but less standardized. For example, a “monthly bookkeeping” subtask could be created with the following four steps:
1.Obtain information from client
2.Governmental Filings
3.Prepare financial Statements
4.Final Review
In the case where you have monthly clients with no governmental filings you could delete the extra sub-task after creating the main task for the client.
Next year, when you clone chose the option to "Clone Last Year's detail tracking information to next year including staff assignments, when detail tracking is implemented at the master task level". This option preserves the unique steps you have assigned to each client. If you select the first option the master template will override the current template used.
If you need additional assistance, then please create a support ticket so that we can contact you directly.