Update references leaves project files without any references

Description

Environment:

• Visual Studio 2017 Professional, v15.3.3, v15.5.1, v15.5.2
• Paket 0.38.3
  When I hit Visual Studio / Tools / Paket Dependencies Manager / Update all packages
  the update process starts and finishes seemingly without errors, and the paket.lock file correctly updated.
  But checking changes made to files shows that all the references are removed from .csproj files.
  There are multiple developers working on the same project, the issue affects us all.

Repro steps

(Don't know if it happens on any othe VS solutions, but in our case:)
Hit Visual Studio / Tools / Paket Dependencies Manager / Update all packages
the update process starts and finishes seemingly without errors, and the paket.lock file correctly updated.
But checking changes made to files shows that all the references are removed from .csproj files.

Expected behavior

References should be left intact.

Actual behavior

All refrences handled by paket are removed completely.

Known workarounds

After the update, using source control compare, restore the unwanted reference deletions.

Start with the Visual Studio Paket Dependencies Manager flow for “Update all packages” and compare the resulting paket.lock and .csproj changes. Reproduce the update and confirm that Paket updates paket.lock without removing Paket-managed project references from the .csproj files.