Theoretically, yes. Not sure how to actually merge title information from two profiles (you could probably find information with google), or how to merge backups effectively, but moving backups from one profile to another is kinda easy (as I learned recently, when I had to transfer them due to a glitch). So, assuming that all of the profiles were made on the same system (or any system that its data was moved to by System Transfer), but on different cards, and you’re transferring between profiles via PC…

First, follow these three steps:
1) Back up your SD card to your hard drive, in an easy-to-find location, without actually modifying any of the files or folders in the “Nintendo 3DS” folder.
2) Make sure your SD is backed up. If not, return to step 1.
3) If you skipped steps 1 and 2, punch yourself in the face and return to step 1.
Yes, backing up is really that important. You’re going to have to muck about with the 3DS’ SD card file system AND some of the system data, after all.

Backups are stored in the folder “Nintendo 3DS\\\backup”, where ID0 and ID1 are the 16-byte hexadecimal folder names (the two-layers-deep gibberish ones that hold your actual stuff). The save-data backup database is in one or more of the files in “Nintendo 3DS\\\extdata\00000000\00000210\00000000”, but I’m not sure which [folder 00000210 is for System Settings extra data for North American systems; note that if you have a Japanese system the folder is “00000200”, and if you have a European system the folder is “00000220”]. So, to transfer your backups from one profile to another, you copy the contents of the “backup” folder into the new profile’s “backup” folder, and then overwrite the new profile’s “00000210” folder with the one from the old profile. This should let you see your backups on the new card, I believe.

Now, I’m not sure if this will work for transferring backups from one system to a different system, or if it’ll work if you do a system format and try to restore backups. I’m also not sure if it’s possible to merge backup folders from two different profiles into a single one, although there MIGHT be a way to do so (assuming that the backups are all for different games, AND you have a total of 30 backups or less). If you put a new card in your 3DS (or move all the data off of one card, format it, and put it in the 3DS), let it make a profile, and then immediately turn the system off, you might be able to copy the backups from one old profile onto the new one, then rename the backup folders from the other old profile to continue where the first profile’s left off [see below], then copy them onto it as well. Then, put the card into the system, and access the save-data backup tool in the settings menu. Hopefully, since there’s no backup database, it’ll just check the folders themselves and create the database from scratch. [Note that I’m not sure whether or not this would work. If you have two saves for the same game, I’m not sure what it’ll do. There is a possibility that this could cause damage to your system. You have been warned.]

[Note that backups are numbered in zero-indexed hexadecimal, so instead of being 001 to 030, the folder names are: 000, 001, 002, 003, 004, 005, 006, 007, 008, 009, 00a, 00b, 00c, 00d, 00e, 00f, 010, 011, 012, 013, 014, 015, 016, 017, 018, 019, 01a, 01b, 01c, 01d. Inside the individual backup folders, there’s a folder with the game’s ID code, and the save file is inside it.]

So… if you’re just working with multiple profiles for the same system, it SHOULD be safe to move the backups from one profile to the other. Anything other than that could very easily be dangerous, so be careful.