Unfortunately you made it really difficult on yourself by changing the Lyra files directly.
You will not be able to get any updates from Epic without a HUGE amount of work every single time you want an update. The reason is because they store BPs and UASSETs as binary files, which is terrible and horrible and I cannot say enough bad things about that insane decision they made long ago.
Because they use binary file formats for those assets, your choice is to either never use their assets yourself, and simply treat them as pure examples that you duplicate on your own, OR the other option is to modify their assets, which means you can never get any updates from them without destroying your own work.