We went at this a little backward. In 2005 we decided to go to an EMR, but couldn't decide which one. We understood that old charts don't belong IN the EMR, as "paper under glass" as they just take up space and contribute little to the function of the EMR.
Accordingly we set up a server and high volume, double sided scanner (expensive) in 2005 to scan OLD charts that were scheduled to go to storage. Thus we stopped storing old charts. When we had thinned out the racks of charts in the office we began hauling the old charts from the storage unit back to the office and scanning those that needed storage and boxing up the older than 10 years / inactive charts without scanning. All of that then was shipped to a commercial shedder. All the scanning was done by staff in the 'off' time, when we were not seeing patients. No overtime. (You have NO idea how much of that you have, Dr. at hospital meeting, making rounds, etc.)
In 2007 we went live with Amazing Charts. As per the general wisdom we marked a few pages to be scanned from the current chart and then entered a good bit under PMHx the night before the visit. Lots of work. We kept the old chart and used it with the EMR for the first two or three visits. When we felt we had all we needed (maybe after one visit, maybe not for 6) we sent the remains of the paper chart to be scanned and shredded. After 18 months all the paper charts, new, old, in storage or in the office, were all gone. Tore out the metal racks and moved some desks in the space!
I am not sure the big, double sided high speed scanner was worth purchasing. We ultimately needed multiple sides with small scanners and we could have bought them with what we paid for the big scanner. And the big scanner could scan pristine pages fast as heck, but old dog eared charts? not so much. And staples or paper clips? REALLY BAD for the big scanner, which went down several times, then we threw it away. Multiple people on multiple small scanners, (we like the Canon DR 2010-C best) might be the best plan.
Most old charts are scanned using the old systems ID numbers, (we started 2 years before Amazing Charts) and now we sometimes have old records that get scanned but have no old number, and little need to be in Amazing Charts, so those get scanned with the number "ACxxxxx". (records from an acquired practice for example) In the demographics, under "other" we record where the old records are, and they can be opened with a program called capture perfect that comes free with the Canon scanners.
That aspect of the whole thing works well.