I’ve pretty much ignored glyphs so far, but I’ve found a greater glyph just now reasonably early in the game and I’m tempted to try it out. But I don’t want to waste it entirely when I upgrade my gear in a few levels.
Are glyphs kept intact when I upgrade gear like the witcher set? Or are any socketed glyphs destroyed?
When the items are upgraded, your runes are kept with the gear, so it will not be wasted. Your rune will stay in effect for the duration of that item.
However you cannot remove the glyph and keep it intact without dismantling the gear in question. If you just want to remove the rune upgrade, then you can keep the item, yet your rune will be destroyed. It is either rune or gear.
Here is a handy tip sheet that has addressed a bit of this.