I would suggest trying to use the replaceDataSource method to convert from a shapefile to SDE, although I'm not 100% this transfer will work as you would need to test it first.
If replaceDataSource does not work, then I would suggest using the UpdateLayer method which would definitely work, but you would need to have the lyr files preprocessed and if different mxds have different symbology for the same shapefile you would either need to create multiple lyr files for the same shapefile source or have all new SDE layers have the same symbology which your end users might object to.
I would also run the script with logging to get an inventory of how many layers you will need to resource before you actually run the tool to process layers on the production mxds.
You could also use the Set Data Source(s) in ArcCatalog on each mxd and resource the shapefiles with that method (This would avoid having to do any programming but could be time consuming if you are dealing with at least 100 mxds).