Protobuild keeps resetting my solution file to "original" one after resync

Unfortunately Visual Studio has no such option.

The flag you want on the command line is --resync, not --generate. Generate discards changes made to .csproj files, while resync synchronises the changes back before regenerating.

For the warning, add the <NoWarn>1591</NoWarn> tag to the <Properties> section of your .definition file (under Build\Projects). You may need to add the <Properties> tag first. Something like this:

<?xml version="1.0" encoding="utf-8"?>
<Project Name="..." Path="..." Type="...">
<Properties>
  <NoWarn>1591</NoWarn>

Then run resync again.