Check out the changing storage type page on the wiki.
Essentially you export the permissions you currently have to a file, then shut down the server. Go to luckperms.conf and change
storage-method-"h2" to whatever you want. I changed mine to yaml. Next you start the server back up and import the permissions from the file you exported earlier. This will re-generate any permissions you had before in the new format.
After I did that there were several yml files created in my luckperms folder that I was able to edit manually. The main thing if you're going to edit permissions by hand is that you still need to use the
/lp commands to generate the groups / parents / tracks before the yml files are created (each group, user, track, etc. has it's own yml file). You'll also have to do
/lp sync to reload the luckperms plugin or restart your server after you've edited a permissions file to apply any changes made.
From my luckperms.conf:
# Which storage method the plugin should use.
# Currently supported: mysql, postgresql, sqlite, h2, json, yaml, mongodb
# Fill out connection info below if you're using MySQL, PostgreSQL or MongoDB