kudu: Code on server not being updated after deploy

I tweeted @davidebbo about this, and he said to post it here. For some reason on my azure website development slot, when i push new code, it runs the deployment, but it’s for an older version of the code than the one in the commit. I can’t publicly post the code/repo, but I can share the details in a private medium.

For example, my global.json looks like this:

{
    "projects": [ "src", "test" ]
}

However, in the deployment output, it says this:

D:\home\site\repository\..\helpers-dotnet\src\***\***.xproj.metaproj : warning MSB4046: Error reading project file "..\helpers-dotnet\src\***\***.xproj": Could not find a part of the path 'D:\home\site\helpers-dotnet\src\***\***..xproj'.

Which was a project reference that used to be in the global.json, that i removed several commits back. Also another weird side effect is that even though the deployment runs, and is valid, it gives me this error on every page of the web app

You do not have permission to view this directory or page.