Yeah, I've done something like this last night. Originally I had a New 3DS with 9.2.0-20J sysNAND and a region-changed 10.7.0-xxU emuNAND haxed through menuhax. At last I got an A9LH haxed console with an 10.7.0-xxU sysNAND CFW and got my games and programs remained.
Briefly, do the downgrade and OTP getting steps using a new region-correct(in your case, JPN) emunand(IMPORTANT I think) until get A9LH in your sysNAND. Then inject your region-changed emunand into the sysNAND using CTRNAND injection method said in the Tutorial part V.
My detailed steps would be like this:
First, I backup my region-changed emunand using Emunand9 and copied all files on sd card to my computer;
Then I formatted a new emunand and followed that tutorial from Part II to Part IV till the last step in Part IV "restore the emunand with emunand-original.bin". Here is what I've done differently from the tutorial, in the last step of Part IV, I restored the emunand with my region-changed emunand backup. And I copied the folder in "Nintendo 3DS" corresponding to the region-changed system (folder with a long code name, usually the biggest one) from the sd backup I made to the sd card.
At last I followed tutorial Part V and installed A9LH on my sysNAND and injected the four parts(like CTRNAND, AGBSAVE,TWLN,TWLP) of the Emunand into A9LH haxed sysNAND. Then it's done! Now your region-changed emunand is injected to your A9LH-sysNAND and your pre-installed games are still in the NAND.
Till now I found no other drawbacks doing like this, except I can't use my E-shop like before, which is a common problem caused by region-changing.(There maybe a thread about fixing this, but since I never use E-shop, I did't do the fix)