Our continuous delivery set-up, until recently, was delivering Service Fabric packages using the following command:
msbuild SFApp.sfproj /t:Package
We have had the exact same problem as you had and I have been looking around for a solution all over the web and did some experiments. Those are the steps that worked for us:
msbuild.exe SFAplication.xproj /p:Configuration=Release /target:rebuild
msbuild.exe SFAplication.sfproj /p:Configuration=Release /target:Package