You'll probably have to loop through the files, and for each one, call a function to fix it.
In the function, you probably have to create an object of type DTS.Package, and call its LoadPackage routine, giving it the filename. Then you have the DTS.Package object read to be edited, and then, I think the package object has a connections property, so probably you loop through all the connections, adjusting some property on each.
As you can guess from how fuzzy I am on the details here, I've not done this.
I think you could do the whole thing in VBA or VBS or VB, probably.