I would update your Fusion Version before moving any further. I believe that 25B is the latest version for CE5 MC9090s. You can even go so far as to push the Fusion update to the devices by way of an Avalanche Package install. You can create a Avalanche Package using the Package Builder that will self extract and install a cab based Fusion Installer automatically for you.
This link practically walks you through the entire process as the example they use is actually for a Fusion 25B install.
We actually have numerous different MC9000 scanners including WM5.0,WM6.6,CE5.0 and CE6.0 I wanted to get this working on at least one newer scanner before I attempt to update the drivers on older hardware. Our MC9190s are running the 25R patch and their settings were initially loaded with a registry file. My test case is a WM 6.5 MC9190 I have created a network profile and pushed it to the device. When I look at avalanche on the scanner the settings show up. However, the wifi radio still connects to the old settings, even I do a warm boot. Am I better off to just replace the existing registry file with a new one?
If you're using a version of the Avalanche Enabler >5.3.38 you could likely take advantage of the Network Property "RemoveOtherProfiles" in order to delete the existing profile created with the registry keys. This solution may still be only temporary as the Registry keys can get remerged upon cold boot of your CE based devices. Your best bet would be to use this setting in conjunction with the removal of the .REG files on the device.