Don't know how much experience you have creating templates so forgive me if you are a pro because this is a basic problem to new users. The Template saves the custom properties not the Sheet Format. So if you changed all your variables and saved the sheet format you didn't save the variables.
Also when you save the template make sure under your properties the sheet format is the one you want at the Location you want.
If that's not the reason when you say "old custom property variables are imported". Imported where? To the Custom or Config tab or somewhere in the vault. Do your new variable show up?
Thank you very much for the response. I always hope people assume I know nothing because there could easily be something I have missed.
I believe I have figured out the problem. I found empty text within the format which was linked to custom properties. It seems that this will auto-create the properties in the custom properties when reloading the sheet format:
So I hope this will help others when they have mysterious properties added when reloading a format.