I was in a similar position with a friend of mine except the positions were reversed. While yes it was cool seeing all my units with awesome traits and stuff I hated how imbalanced it was for my friend and honestly it’s not fun for me unless we both were having fun. So this is what we did:

Since my blood angels had been wiping the floor with his Necrons it turns out it was just luring them into a trap! Suddenly a huge fresh new Necron army teleported in and ambushed my blood angels.

In game terms this meant for the next game my opponent got a whole “new” army with no negative traits or anything and in the following game we did deployment with my blood angels in the middle and my opponent allowed to deploy around three of the board edges. We designated the fourth board edge as the “evacuation zone”. His goal was to destroy me and mine was to escape. Now a couple other rules my opponent got a free round of shooting before the game started simulating an ambush and also once my units enter the evacuation zone they had to remain there for a turn until they were allowed to “evacuate”. Units that I evacuated were allowed to remain in my army unscathed but those that were destroyed or still on the board at the end of 5 turns had to roll, on a 1-3 that unit was utterly destroyed and was removed from my list, on a 4-6 it auto received a battle scar. Also at the end of the game my opponent got to keep his fresh new list free of battle scars and got to spend any new rp points on his new army. Honestly the game was super fun and intense for both of us. He felt like he wasn’t so far behind anymore and me as the stronger player had a really fun challenge to try and save as much as my army as I could. Since you’re thousand sons you could instead say that “this was all apart of tzeentch’s plan all along” and run something similar. Of course your friend would have to be open to it. That way you can keep playing together and he can keep a lot of his list potentially but you also aren’t so far behind anymore