I've edited my bouquet to have the correct channel numbers as of today but some channels don't appear in my custom bouquet.

I did this as you instructed: Menu > Setup > Tuner config/Service searching > AutoBouquetsMaker > Update config files
But I get this error: "Incompatible versions: 2.5 > 2.9"

I have Vix 4.2.030 and a VU+ Duo 2.