It's the expected behavior. Dotfiles in your home folder usually have global settings, so having more than one is a bad practice.
You may have your common rules in it, and then in the directory where you have each ledger file (e.g. `~/work` and `~/personal`) you can have another `.ledgerrc` with specific settings for each project if you need.
Also, instead of sourcing many files with `--file` you may use
includes in a main ledger file, e.g.:
include accounts.ledger
include 2022.ledger
include 2023.ledger
include loans/friends.ledger
Then you just have to specify this file with `--file` and all the others will be included as you want.
This could even simplify your two `.ledgerrc` files down to a single one, because if you specify e.g. "--file main.ledger", I think it should work in both directories.