First- after upgrade of Xenforo - It WONT overwrite a modified template?
Can you explain the template merge option when upgrading Xenforo? When I merge it WONT effect modifications I made to the template? Just merge the changes to the non-modified sections of the template code?
It will not overwrite the template no. If it can auto merge, it will place any changes into the template. If it cannot auto-merge you must choose your modifications, XenForo's, or a defined combination of both.