I have created a template Kanban board to use to track new customers through the on-boarding process, but if I remove sub-tasks from a particular board that has been copied from the template it removes them from all boards.
Boards are not containers for issues, they are a view.
If you do something to an issue, whatever you do will "affect all boards" because you're changing what the boards are showing you, not the board.
If you don't want an issue to appear on a board, you have to change the issue so that the board no longer selects it OR change the board so it no longer selects for the issue.
@bnxw, when you say you have a template board, I assume you mean that you are copying each Kanban board from the same one, yes?
If so, the issue you are likely running into is that all of the Kanban boards are using the same filter. Because of this, when you modify the filter on one board, you are modifying the filter for all the boards.
To address this, you should change the filter on the board you want to remove subtasks from to a unique filter. You should be able to copy the template filter and then modify it to remove subtasks. Then associate the new filter with the board you want subtasks off of.
EDIT: I assumed when you said "Remove" you meant that you modified the filter to prevent subtasks from showing. But you could have also meant that you have deleted subtasks from a board. If that is the case, deleting a ticket removes it from the system as a whole. Boards just give you a through which to view tickets. If you delete a ticket it cannot show on any boards.
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