Dealing with schema.rb changes when merging jumpstart updates

I wonder if you can help me.

When I try to merge the jumpstart updates I occasionally get foiled by what to do with the schema.rb changes.

In adapting the template to meet my own needs there are obviously changes but I can't seem to just delete the scheme and recreate it ... or can I?

Any help would be really great!

If there are conflicts in schema.rb and there is a pending migration. 
I usually just just delete the contents of schema.rb and then run the migration so it populates it properly.

Not 100% sure if this is the correct way to go about it!