As a limitation of how workspace integration is implemented in vscode-wasm, the workspace structure is fixed upon the WASM module's initialization phase. Specifically, the folder list is mapped into WASI preopened file descriptors and cannot be changed when the program executes. If the user opens or closes some workspace folder later, it is impossible to reflect changes to WASM module's file system. The mismatching can cause user confusions. The best we can do for now is to kill and respawn the WASM module.
It is possible to make the list dynamic in vscode-wasm by providing a single root, not mapping each workspace folder to a preopen fd, but I do not know whether it is an easy task.