Can we manually change recurring payment subscription statuses in the database if they're no longer linked to their original membership?
More frequently than not I find myself tweaking records in civicrm_contribution_recur precisely for the reasons you mention.

You will need to be sure, however, to account for any amounts not collected and perhaps create new recurring contributions or pledges so that those amounts are not entirely lost. Depending on how payments were recorded after the subscriptions became dysfunctional, this might be a lengthy task.

In the case of dysfunctional subscriptions, updating the the contribution_status_id to whatever is appropriate should not impact anything else.

Regarding recurring contributions associated with memberships - contributions per force must have a financial type, this would be the financial type used to create the subscription, so there should never be a case where money doesn't get allocated somewhere, there would indeed be a problem on reporting financials if this were not the case - could you clarify further?

Hope this helps,
Tamar