Hi ebvt , is quite logical that when you change theme of icons, some icons disappear, that's because that theme does not contain the icon of these applications.
Because there are a few icons to personalize them in ItaskNG ?.
Example:
Look for an icon theme that you like, choose the icon you like for the applications to be used in ItaskNG , keeps those icons in a folder (Icons ITask) at his home, now just right click the mouse and select Edit icon, Icon tab, click in image icon and select icon in the folder you created in your Home, Apply tab.

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Greetings:
Agust