I would imagine if your practice is hospital based, that there are some type of resources available to assist you. Maybe you belong to an IPA that could assist. This is such a concern to me that even if you don't have a standard practice attorney, I would hire one to review this issue. To me, the billing issue is actually the lesser issue here.
This is in NO WAY official advice, but if I was the person making this decision:
1) I would first make a thorough search for the records that were completed on paper. Perhaps they were all scanned into a particular file and not uploaded to the individual charts. Who took those papers from you and where did they go from there?
2) If the paper records are all indeed lost, from a patient care perspective only, I would make some attempt to document what you could. Something like a standard sentence in the beginning of each document with something like:
This note is being re-created on a later date due to a computer systems error resulting in documentation unable to be located. The documentation below reflects the services that took place to the best of my recall.
Followed by whatever the clinician can remember about the patient/encounter. For your ongoing patients, this will be better than nothing.
3) I would not bill those services to insurance unless advised by compliance, an attorney, or the insurance company, IN WRITING.
Good luck!