We're using this to sync 1 of our Jira projects which has 4 scrum teams and hence 4 scrum boards. Each one also has its own story map. Importing the project means we have to manually remove unwanted stories and reallocate them to the relevant story map once they've been imported, luckily we've done this at the start of a new project and there's only 30 or so stories. If we had done this towards the end of the last project we would also have imported around 10,000 stories and the manual removal could've taken a few weeks.

Our main Jira project contains more than 10 000 stories. At a minimum, we must be able to filter stories to import. A JQL query could give us all the flexibility we need.

At a minimum, I would like to be able to sync a board to either a version or an epic, instead of to a project. We have the same problem, multiple initiatives in a single project.

We have one single Jira project and split our teams using a custom field. We use both project and the custom field in the JQL for our Agile boards in Jira. We need to be able to sync to/from storiesonboard using this same JQL string. It should also be used for all stories created by storiesonboard when creating new stories on sync down to Jira.

In short, we have the opposite problem, but the same solution of being able to specify a JQL query for the sync would solve both of our issues. Using JQL is really the general solution. You can't assume the project field is all you need or if it's even needed at all. Allowing admins to specify the JQL solves it.