Assets and code removed on readding an extension and creating conflicts

[srietkerk]

Upon adding an updated extension to a project, a user of ours saw that code and assets unrelated to the extension were removed from their project. The only code that should be removed from the project is the extension itself.

To Reproduce
Steps to reproduce the behavior:

1. Go to arcade and open a project
2. Add an extension to the project
3. Update that extension
4. Add the updated extension to the project to "override" the previous extension
5. Encounter problem

Note
It's possible that this will only happen on larger projects.

Reference: https://forum.makecode.com/t/half-of-assets-gone-and-2000-blocks-of-code-but-i-can-replicate-it/29344