Relative flake inputs since 2.26 don't work as expected

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Hi,
in nix 2.26 relative flake inputs got fixed so they work better than before.
I just switched from version 2.25 to 2.28 and because of this change my config doesn’t work anymore.
Before I manually updated the relative inputs and trough this process it worked.
But since the update my config is broken and I can’t get it running again.
Here is a minimal example of my issue:

structure of my monorepo config:

.
├── flake.lock
├── flake.nix
└── packages
    ├── my-package
    │   └── flake.nix
    └── packages-overlay
        └── flake.nix

my-package is just a derivation inside a flake.
In packages-overlay I import all package flakes and accumulate them in an overlay:

{
  inputs = {
    nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
    home-manager-switch = {
      url = "path:../my-package";
      inputs.nixpkgs.follows = "nixpkgs";
    };
  };

  outputs = { my-package, ... }:
  {
    overlays.packages = final: prev: {
      my-package = my-package.packages.${final.system}.default;
    };
  };
}

Then I use this overlay in my final flake, in this example I just create a devShell from it:

{
  inputs = {
    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
    packages-overlay = {
      url = "path:packages/packages-overlay";
      inputs.nixpkgs.follows = "nixpkgs";
    };
  };

  outputs = { nixpkgs, packages-overlay, ... }:
    let
      pkgs = import nixpkgs {
        system = "x86_64-linux";
        overlays = [ packages-overlay.overlays.packages ];
      };
    in
    {
      devShells."x86_64-linux".default = pkgs.home-manager-switch;
    };
}

I then start the devShell by executing:

$ nix flake update && nix develop
error:
       … while evaluating the attribute 'my-package'
         at /nix/store/6k0ca7dm8kqjdgn6892pm3s0hl6rmvw5-source/packages/packages-overlay/flake.nix:13:7:
           12|     overlays.packages = final: prev: {
           13|       my-package = my-package.packages.${final.system}.default;
             |       ^
           14|     };

       … while evaluating the attribute 'my-package.result'
         at «flakes-internal»/call-flake.nix:98:7:
           97|     {
           98|       result =
             |       ^
           99|         if node.flake or true then

       (stack trace truncated; use '--show-trace' to show the full, detailed trace)

       error: path '/nix/store/6k0ca7dm8kqjdgn6892pm3s0hl6rmvw5-source/packages/packages-overlay/packages/my-package/flake.nix' does not exist

Before the version change I used this before running it:

$ nix flake update my-package --flake ./packages/packages-overlay

To pin the realtive path afterwards executed the devShell and everything worked.
I guess I have to change something about the configuration, but I don’t know what could be the issue.
I already know the section about path in the manual.
Could somebody please point me in the right direction?