How can I rebottle my kombucha without losing carbonation?

I've been giving brewing my own kombucha a try, following this guide. It's been going well, and I've made it all the way through my first batch! \o/

The one bit where I differed from the guide was in the last fermentation, where I also add in the flavors: instead of using flip top fermentation bottles, I used mason jars. I did this because I didn't want the final bottles I'd drink from to have bits of fruit, etc., so I'd do the flavoring and final fermentation in the mason jar, and then strain the actual kombucha into individual bottles for drinking. By doing this, though, I think I lost a good bit of the carbonation from the last fermentation... which is not ideal.

Are there any ways to effectively rebottle kombucha without much loss in carbonation?