I had the same problem. Impulse allowed me to update Sins but told me I had to uninstall Entrenchment, which caused Sins to be uninstalled. I can reinstall Sins but then Entrenchment (0.92.005) claims it is installed and it needs to be uninstalled again, and the entire process loops itself... First Sins uninstalls, then Impulse moves on to uninstall Entrechment and gets an error msg: "There is an error in XML document (28,8)." What seems to have helped was to 1) ensure all files in Sins directory were deleted 2) restarting between reinstalling 3) clening up registry via Norton WinDoctor before reinstalling and 4) installing Sins through clicking on Install Entrenchment, which caused Entrenchment to be downloaded and preped for installation by Impulse while main Sins was still donwloading. One or more of those steps presumably got rid of the old Entrenchment instalation artifacts. Update: at least, that's what I hoped. I've restarted the comps and now I have something different: Entrenchment is installed, but Sins claims that the main game is not! Aaargh...
Overall, I ended up redownloading and reinstalling Sins 5 times. I hope then when the next expansions comes out, things will go better - I am afraid to think of how messy this may get when Impulse will start playing with more then one expansion... makes me really really not looking forward to helping with another beta, neither.
Further note: I had Sins installed on another drive, now it reinstalls itself to C\Program Files\ giving me no ability to chose where I want it to be installed 
