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I was installing kde when I found out I didn't have the ql in my USE variable. I rebooted the system, added it and emerged kde again. Will this affect anything?
It will not affect anything. Re-emerging will merely compile KDE again (if you can stand the compile times) and everything will be fresh and ready to go.
In fact, updates are also done using the same emerge command as the one used to install.
For example if you used to install program ABC:
emerge ABC
To update ABC also, you use the same command. Nothing shoud break.
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