I have never tried it but I would think that you could minimize carbonation loss by using a racking cane, some food grade tubing and a spring tip bottle filler like you would use to fill beer bottles when homebrewing. Those items are not expensive.
See here:
http://www.northernbrewer.com/shop/brewing/brewing-equipment/bottlingThe process works by siphone and you fill the bottles from the bottom up rather than pouring. I may try it out and report back because I already have the home brewing equipment.
Tim