I'm glad for you although I will reiterate please pay attention to (/do some research on) whatever it is you choose to install on your system
Now what do you mean
I downloaded a few things a second time though. Is that going to cause some issues or just take up some space?
Do you mean to say that you believed your SD card was full before this problem and then you downloaded a few games before fixing your 3DS so now that you have your old titles and your new titles you're wondering if they'll still be fine... Of course you're fine it's not as if your system overwrote one game with another and simply because you weren't able to see it... FYI you need about double the space of a CIA to install it so it could be that the games you installed later we're just smaller than the games that you installed previously
Or do you not even have access to the new games you installed due to the fact that you you switched back to your old 3ds folder and the games reside in your new 3ds folder if that's the case you can simply use the bank application again to switch back to that new 3DS folder and delete the games from there to save space on your SD card the switch back to your original 3DS folder and install them there.
If you mean you installed the same exact games on your system while it was quote screwed up that you had on it before it was messed up then while it will cause no issue it will eat at space on your SD card you need to go back to the new title ID folder and delete those games unless you're okay with them taking up space for no reason on your SD card