i'm never 100% positive until the culprit is found and has admitted its bug.
But I'm not going to spend 4-5 hours for free (and off development tasks) checking everything and troubleshooting if there is a consistency doubt, or another possibly associated bug:
Thus, before anything else:
How exactly did you delete the plan ? which very exact steps ?
Are you able to reproduce using those steps to delete a plan with subscriptions in place ?
We need to be able to reproduce.
To answer your question:
Free users of CB will be kept if you uninstall + delete cbsubs tables, but memberships, and all payment records, and settings will be gone.
But please do that only after having reproduced and listed one by one ("click exactly here") the steps to delete a plan with existing subscriptions...