In the case of Skype, your right: Skype can probably change their protocols and ruin the work of the reverse enginners. But this would have a price: Skype users would have to install the last version of the client to be able to communicate with their contacts. If Microsoft started to modify the Skype protocol each week, the users would probably get tired of updating their client weekly and they would use another software.

For others proprietary softwares, breaking the compatibility with old versions is hardly conceivable: If Photoshop or AutoCAD where suddenly unable to use read and write the terabytes of data created by their users, those users would probably throw their PC through the window and never buy again a proprietary software...