System dbs have different collation

I have installed an instance of SQL Server 2016 SP2 called DNF containing 2 DBs and also the system DBs. After providing the instance to the dev team, they realised that they need to change the collation. They changed the collation for the 2 DBs by themselves and asked me to make the change for the system DB. I took a backup of all databases and rebuilt the system DB. It works fine and all the dbs changed to new collation. I made a mistake by restoring the msdb, model and finally I tried to restore the master. I succeeded to restore the model and msdb and faced a lot of issues when coming to themaster. I ran the query select name, collation_name from sys.databases and found that the model and msdb have the old collation, and this is logic and was a mistake from me. I tried to rebuild again, but collation refused to change on model and msdb and found the sql server and sql server for the instance stopped and won't start anymore. The situation now is : master and the 2 non system DBs have the new collation and model, msdb have the old one, and the services won't start. What is the way to solve this issue? Does an instance repair will solve this issue? Or there is something else that I can do? .