The minified content of index.js is write to both index.min.js, and modal.min.js, that contains same name of parent folder of index.js
Step to reproduce
1 - Set config "minify.minifyExistingOnSave": true
2 - Create structure like screenshot above
3 - Edit and minify index.js
The content minified of index.js will be written to both index.min.js and modal.min.js.

Result after minification

Minify: 0.4.3
OS: windows 10 Build 19041.572
VSCode:
Version: 1.50.1
Commit: d2e414d9e4239a252d1ab117bd7067f125afd80a
Date: 2020-10-13T15:06:15.712Z
Electron: 9.2.1
Chrome: 83.0.4103.122
Node.js: 12.14.1
V8: 8.3.110.13-electron.0
OS: Windows_NT x64 10.0.19041