I haven't tested this with .3ds files, but you could theoretically combine them into a single .3ds using the command line in Windows. I used to do this with PS2 ISOs that were split into multiple files without issue, so it may also work with .3ds.
1. Place both files in the same folder.
2. Open a command prompt window and go to the directory with the two files
3. Enter the following command: copy AYTE.3d* AYTE.3ds
4. Move the newly created .3ds to your mSD
5. Hopefully, it should recognize it as a valid rom.
EDIT: You should be able to rename them without issue so long as each file has the exact same name before the .3d0/3d1