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.