Upgrades still delete user npm modules

Wappler Version : 4.6.1
Operating System : Mac OS X
Server Model: Node
Database Type: MongoDB
Hosting Type: Local

Expected behavior

What do you think should happen?

Upgrade to a new version and all my installed node modules are left alone

Actual behavior

What actually happens?

When upgrading it still deletes my module

How to reproduce

Install jsonwebtoken and upgrade, and the module goes missing

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