No Ein. Bad dog.
First, you must cycle past the game you want to backup making sure that you wrote the savedata to the mSD in the Sky3DS.
Then, make sure to backup savedata for each game individually.
Then backup the ROM as well. (especially for NAND or EEPROM-NO games like Pokemon)
Now, you may freely delete the game in Diskwriter. When you write it back, make sure you write back both the backup ROM and the SAVEDATA for it.
Done.
OR!!!!!!
You can just put the game into RESERVE if you're using Diskwriter 2.0.2b1. (not sure if they released a newer update... let me check... oh wow, region four and another template) and then just put it back into POSITIVE and the savedata will remain intact (as long as you cycled past the game after playing).
So, let's recap:
after playing game...
CYCLE PAST GAME (just press blue button and wait for LED to stop flashing)
BACKUP SAVEDATA
BACKUP ROM
RESTORE ROM
RESTORE SAVEDATA
or
CYCLE PAST GAME (always)
PUT INTO RESERVE (store but not play)
PUT INTO POTITIVE (puts in 31 playable cycle list)