Best practice to split configuration about impermanence

[coritanic]

Note: This isn't relevant in this repository since it's a Nix language thing. You should normally ask this in NixOS Discourse's help section. But since you asked:

Nix merges the same attributes when found in separate files. This isn't the case when the same attributes are found more than once in a single file (e.g. 2 environment.persistence."/cache" in one file).

There is no best practice for what you are asking, different people do it differently. The most straightforward way is creating different Nix files for different applications and importing them in configuration.nix (same way as hardware-configuration.nix).

If you want to keep it in one file, you would do something like this (adjust to your configuration.nix):

{ config, lib, ... }:
with lib;
{
  environment.persistence."/test" = mkMerge [

    {
      hideMounts = true;
      directories = [ "/testdirs/regular1" ];
    }

    { directories = [ "/testdirs/regular2" ]; }

    (mkIf config.services.nextcloud.enable { directories = [ "/testdirs/nextcloud" ]; })

  ];
}

Same attributes can be merged in a single file with mkMerge without causing error.