You won't lose A9LH doing system transfers. If I'm understanding you correctly, you have your games and saves on your first system, but you'd like A9LH on it as well, and you have a second system with the A9LH that you'd like on your first system. There's nothing stopping you from doing this. Here's how:
1. Transfer from your first system to your second system. After this step, your first system will be reformatted while your games and saves will be on your second system... With A9LH. You may need to reinstall FBI, but A9LH will still be there to let you run Luma, decrypt9, and hourglass9, so that won't be a problem.
2. Purchase a game compatible with DSiware hax (if you haven't already) on your second system.
3. Use the guide linked above to prepare your DSiware game for use with DSiwarehax.
4. After a week passes (Nintendo only lets you perform a system transfer once a week) transfer back from your second system to your first system. Although this resets your second system, A9LH will have still survived, allowing you to reinstall FBI again if you want or even restore from a NAND backup if you made one earlier. But the point is that your games and saves will be back on your first system, now including your DSiware game with the DSiwarehax payload.
5. Perform DSiwarehax on your first system and follow the A9LH guide to install A9LH.
Just a few things to keep in mind.
1. You can't transfer from a N3DS to an O3DS. If either system is a N3DS, they will both need to be or else you won't get anywhere.
2. Anything that you install as a .cia or anything from apps such as Freeshop are lost during a transfer, which is why your DSiware game needs to be purchased from the eshop. After you're done, you can reinstall anything that didn't transfer.
I'll add more if I think of more. Just writing this of the top of my head. [emoji12]