Any natural carbonation will be knocked out during the filtration process. It's advised that you degas your cider before you filter, this helps the filtering process go much faster.
I've tried fining agents and I'll never use them again. In my experience they strip out alot of flavor.
I'm playing around with using pectic enzymes and treating the juice 24 hours before pitching the yeast.
By doing this you will have gotten rid of most of the dead yeast load sitting at the bottom of the tank also and far enough away from the end of the suction of the racking tube.
Best regards
Chris Rylands
you may try to let the fermentation complete, and let your cider drop clear using enzymes or cold temperatures. Then when it's clear rack it out , clean your tank, and rack back into into your combo tank being used as a spunding tank. Add 20% unfermented juice or some sugar for carbonation to the appropriate specific gravity to get meet your carbonation level.By doing this you will have gotten rid of most of the dead yeast load sitting at the bottom of the tank also and far enough away from the end of the suction of the racking tube.