Hey Adam,
I could also try to handle this in my program (do a move upon program start), but it would still inflate the size of the update because wyUpdate would think they were new files.
Honestly, best way to handle this is to leave the files in place, build the update patches as is (that is, assuming the old files will stay where they are), and execute a small batch file as part of your update that will copy the old *.dat files to a folder you specify.
If the user updates from v1.0 to v2.5 and my 'archiving process' was only implemented in v2.0 then they would skip it.
wyBuild currently (as of 2.6.x) implements only direct patching (that is, a patch is made for all old version to the latest version). We're adding the option of incremental patching (wyUpdate will install all the intermediate versions to get to the latest version) in wyBuild 2.8.
With direct-patching, any action you want to take that's mandatory must be taken with every new version. So add the batch file to every new version and set it to execute before the update take place.
In wyBuild 2.8 onward, if you select incremental patching, you'll be able to set it to execute once for that version and all users will inevitably execute that file as they update (because wyUpdate will download & install all intermediate patches).