With the new Software Developer toolkit, the crmregister file often gets amended simply through the process of opening and closing Visual Studio.
See the screenshot below - I checked the crmregister file into VSTS, closed Visual Studio, re-opened it and the entire workflow assembly section has been wiped.
Sometimes both plugins and workflows get wiped.
This means that the first thing you have to do every time you open the solution is check whether any changes have been made to the crmregister file and undo them. If you had not checked your changes in, you may lose them altogether.
