No.
As far as I'm concerned, ST XI won't have to be reconciled with continuity.
Continuity will have to be reconciled with *it*.
Any discrepancies can, and will, be dealt with, without reboots or any crap like that.
I don't care how different ST XI looks from TOS. Being the latest, I consider XI to be definitive. As far as I'm concerned, history always looked like that.
As far as I'm concerned, ST XI won't have to be reconciled with continuity.
Continuity will have to be reconciled with *it*.
Any discrepancies can, and will, be dealt with, without reboots or any crap like that.
I don't care how different ST XI looks from TOS. Being the latest, I consider XI to be definitive. As far as I'm concerned, history always looked like that.

I'm confident, from what I've read so far, that there won't be any major continuity problems that will bother me. As long as it's better than any of the other Trek movies ever made, I'll be well-content. 