Because the all the data is transfered to the target system, the old one becomes formatted. Also there is a 7 day waiting period before any system transfers can be done again with the two systems.
If you using the field runners hax. Simply buy it on hacked 3ds, perform system transfer, downgrade system then install the a9lh hax, wait a week then perform system transfer again. Which to me seem like safest option
Is better to just wait until system transfer is back again before actually using the system for playing games or online modes for easy and simple reasons.
I seriously have no idea what you are talking about, i thought your problem was how can you perform system transfer without wiping cfd 3ds. If you wanted help installing a exploit you should have said that instead of what you put as the title.
Or posted this in the noob paradise section or which ever section pretains to what you need help with.