I have two "branches" of groups named "donation" and "level", the first one have a role as rank, the other one is for level up plugin. First time player joins he has default group and when player has enough exp command executes: /lp user {user} parent settrack level l_X. Of course I use that command for donation also in order to not reset other parents, like parent set does. So, when level track set, user have default primary group, default and l_X parent groups.

The problem occured today, when I restored some donate ranks on people, who had default as primary and +some l_X as parent. I executed something like that:
/lp user {user} parent settrack donation premium

After that player has l_X as primary group and l_X + premium as parents. And from that point I can't even change primary group, switchprimarygroup notify me, that player already has that group as primary, but that's definitely not, and even in H2 database all players have default primary group. Command ... parent set works on primary group, but I can't use it because I will lose level track. What can I do now?

I fixed that with setting weight to all donation groups to 1.

Sorry I just forgot to reply to this - as you've worked out, primary groups in this case are being determined by weight. :)

https://github.com/lucko/LuckPerms/wiki/Configuration#primary-group-calculation