VSCode rust-analyzer -- Looking for files from different projects in each other's folders - "File with cargo diagnostic not found in VFS: file not found:"

rust-analyzer version: (eg. output of "rust-analyzer: Show RA Version" command, accessible in VSCode via Ctrl/⌘+Shift+P)

rust-analyzer version: 0.3.1258-standalone (43fb9563b 2022-10-23)

rustc version: (eg. output of rustc -V)
rustc 1.66.0-nightly (9565dfeb4 2022-10-28)

I am getting errors like these:

[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\libsfasta\src\masking\ml32bit.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\libsfasta\src\masking\ml32bit.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\libsfasta\src\masking\ml32bit.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\libsfasta\src\masking\ml32bit.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\libsfasta\src\datatypes\seq_loc.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\libsfasta\benches\ml32bit.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\libsfasta\benches\ml32bit.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\sfa\src\main.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\sfa\src\main.rs
[ERROR rust_analyzer::main_loop] flycheck 3: File with cargo diagnostic not found in VFS: file not found: c:\Development\phyloclap\sfa\src\main.rs

These are very weird, as those files should not exist (sfa and libsfasta are folders in a different project, and are not and should not be present in the phyloclap project).

It is referenced as such in Cargo.toml though:
libsfasta = { path = "../sfasta/libsfasta" }

So maybe I am misunderstanding something? I have been trying to debug why I do not get compilation errors in VSCode anymore inline as red, but everything else re: Rust-analyzer is working, and this is the only type of error showing up.

Start by reproducing the diagnostics in VSCode with the Cargo.toml dependency path ../sfasta/libsfasta, then trace the rust-analyzer flycheck and VFS handling mentioned in the error. Done means diagnostics no longer reference files from the separate project and inline compilation errors appear correctly.