Go to File -> Properties -> Update & server files, then change the output folder to "Updates\%version%". This will make every target version have its own folder.
I am using wyUpdate to maintain multiple release of the same product.
Problem is, it appears that wyBuild dumps all the Update files into the same folder INCLUDING wyserver.wys.
So at any given point in time, there is only a single wyserver.wys file and it is for the most recently built updates.
THis makes is really easy to inadvertantly upload updates without building them first which would potentially upload the WRONG .wys file for the wyu's it's uploading.
For instance, if I decide to change the path on my server where my uploads are kept, and then I reupload to that new folder without rebuilding the updates, then I can easily get the WRONG .wys file uploaded.
Go to File -> Properties -> Update & server files, then change the output folder to "Updates\%version%". This will make every target version have its own folder.