So I've installed some apkenv games and made icons to them. Worked well. After few weeks I incepted too deep, and had to reflash. After reflashing I restored backup that I've made with stock N9 backup app.
And here is the problem: the icons to apkenv games have appeared, and I don't know how to get rid of them. I tried installing apkenv-qml, but as I was expecting it does't recognize them.
The source of the problem is obviously in catalogs that backup app restored, but I have no idea where apkenv-qml keeps the shortcuts to games. Help, anyone?

(this is what it looks like)

If i'm not wrong those .desktop files are stored in /home/user/.local/share/applications/

Check that folder and remove any relevant .desktop files. (do not remove quicklaunchbar*.desktop files)

Make a backup of the folder first if you are not sure.

I deleted files named with *apkenv*.desktop and the icons were gone. Case solved, thank you.