On the transform map form, there's a checkbox "run script". Check the box and an input box will open up in which you can enter code that will run for every record in the import set. You can do any kind of server side processing necessary in there. Seems like maybe you have some field mappings that you're coalescing on, and those records are being updated. Well, instead of that, just write a GlideRecord query in the script, and if you find the record existing, use the autoSysFields function to suppress the sys field updates.
