There did turn out to be a slight change in behavior of form deletion in v1.28 that made this error more likely and harder to recover from. We have made further changes that should alleviate this and it's available in beta. We experimented with also preventing downloading a second form with a form_id and version combination already on the device. Unfortunately, we found out that replacing a form with a matching form_id and version has become part of some workflows so we can't do it yet.
Collect has the expectation that a form_id and version combination identifies a unique form. In your case, it sounds like you could generate a random version for each form that you generate? By default, as updates are downloaded, only the latest downloaded version would be seen by your data collectors.