Uninstalling by BBM or SD management won't solve the problem.
Yup, I went through that before.
To fix it,
1. Backup present your SD card
2. Use a different SD and resetup emunand and update emunand to enter eshop
3. purchase the game from eshop (make payment and all)
4. Now you can swap back to the original SD card. you will be able to "redownload" the game now, as you DID make a purchase.
(the error happened because eshop checks 3DS nand and sees that you 'purchased' the game. however when checking nnid database, you didn't, so download fails at 99%)
I encountered this issue just 2 days ago, and had to find the fix myself.
Let me know if it works for you. It worked for me
(I recommended another SD card, so that it would not mess up the files in your present SD card)