csproj file is no longer updated after upgrading project's ToolsVersion #3837

Description

when running paket install, the references in my project files (csproj) are updated according to the paket.references file. This worked fine as long as I was working with Visual Studio 2017 (the projects have set ToolsVersion="15.0").
After upgrading to Visual Studio 2019 (ToolsVersion="16.0"), paket ignores changes in the paket.references file. The references in the projects are staying the same when doing a paket install. However, paket touches the project file (it moves the import directive to Paket.Restore.targets to another location in the file).

Repro steps

paket.dependencies:

source https://api.nuget.org/v3/index.json
framework: net48

nuget StreamJsonRpc
nuget NUnit

paket.references:

StreamJsonRpc

csproj file beginning like this:

<?xml version="1.0" encoding="utf-8"?>
<Project ToolsVersion="16.0" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">

Expected behavior

When I change the paket.references file (e.g. adding NUnit), I expect that a reference to NUnit is added to the project when I run paket install.
(This is actually the case when the csproj's ToolsVersion="15.0")

Actual behavior

The reference added to paket.references file is not added to the csproj file.
Removing references also doesn't work.