It will depend upon the repro you have. Sometimes they are essentially normal carts and respond to save dumping/writing as per usual, or same but for being a flash cart. Other times they are strange alterations of the ROM and use stranger methods. As a general rule we advise against repros for this sort of reason -- they are seldom well made (unless they are a flash cart twisted to that end) and usually have a list of annoyances like this to deal with, as opposed to just getting a flash cart.
Or if you prefer figure out how to dump and rewrite the save, generate whatever you want as far as this save and then write it back. This may or may not be the same as the methods used for commercial carts or flash carts, or compatible with existing save editing software for such games.
If you have a modded 3ds it can dump and write back DS saves easily enough. I am not sure what people are using these days.
You can dump saves well enough with DS flash carts on a DS or DS lite. Some will use wifi methods, others might have a GBA expansion pack, there are some even older things for DS mode GBA slot carts and older things still but don't go there if you don't have that.
If you have a modded DS or DS lite it can do GBA games well enough. Some like
https://gbatemp.net/download/gbaldr-3in1-gba-loader.10977/
There are hardware based methods for all of those as well, though you will probably only be able to buy DS ones these days and will have to build GBA stuff.