If you got a R4 [anything] and want to use the eShop? You can expect to be buying another R4 [anything] after you visit the eShop, end of story.
"But but I heard you can updated the R4 [anything]," that depends on what clone and version of the clone you got. you can dig through the first 2 pages of the section here and locate the R4 threads and see which one matches your. If none, your SOL and you doing what I said above.
Your going to be taking your R4 apart to compare.
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If you really want to avoid things like this, get 2 or more 3DS/XL/LL, that way you got one with a flashcart and another with eShop games.