Before implementing antenna-system changes, carefully follow the instructions in the post,
Lost Channels? The Memory Erase Scan. It's quite possible that the pre-transition UHF channel assignments got "stuck," preventing the tuner from confirming the new VHF channel locations. The process takes about 15 minutes per tuner. That might be all you need to do.
If a "double re-scan" doesn't help, we'll certainly need to know what your antenna is designed to do and what a TVFool report for your location looks like, as Rick suggests.