There are methods to bulk load Windchill.
Files brought into Windchill from disk through Creo will be saved in that version of Creo when saved in Windchill. There is no way around this fact with this method.
If you bulk load files, then they would be imported into Windchill in their current version format.
Definitely, if you use creo to import the files, they will save in to the workspace to the software version used. Technically, it will be a different file at that point than the one on the hard drive.
If you are uploading a lot of files, definitely look in to what Ben is saying about bulk uploading.