What width of tires do you have with the 700c wheels?

How much clearance?

Some photos might help.

I did a conversion of 26" to 700c on one bike. Fat 26" to narrow 700c. It worked reasonably well. Of course, I needed to do changes on the brakes, but your discs should be easy enough to adjust. If you can match the hubs, then the exchange should be easy.

I'd look at perhaps a 650b conversion rather than a 26" conversion. The sizes should be closer if you're using a narrow to mid sized 700c to a mid to fat 650b. Again, assuming frame clearance (and fenders?) is adequate.