I've actually done quite a bit of research into this, both on MMO-Champion's Item Database, and by crafting 10 of EVERY glyph and transferring to the PTR. Most of the glyphs are being changed in Patch 4.0.1. -Most- of them are just getting morphed into the new glyphs. The items are actually changing into the new ones. For example, Glyph of Living Bomb will now be Glyph of Slow. Glyph of Divine Storm is now Glyph of Templar's Verdict.
So if you've already learned all the glyphs, you have nothing to worry about, right? WRONG. Currently there are some glyphs being removed and some glyphs being added. Here's a list.
New Glyphs (12, 3 not learnable)
Glyph of Faerie Fire - Trained, requires 120 Inscription
Glyph of Tiger's Fury - Trained, requires 120 Inscription
Glyph of Death Wish - Trained, requires 150 Inscription
Glyph of Feral Charge - Trained, requires 150 Inscription
Glyph of Blind - Trained, requires 180 Inscription
Glyph of Intercept - Trained, requires 250 Inscription
Glyph of Lacerate - Trained, requires 330 Inscription
Glyph of Living Bomb* - Major Inscription Research
Glyph of Colossus Smash - Book of Glyph Mastery
Glyph of Armors - Not learnable. Confirmed to be bugged.
Glyph of the Long Word - Not learnable. Confirmed to be bugged.
Glyph of Vanish - Not learnable. Confirmed to be bugged.
Removed Glyphs (17)
(Death Knight) Glyph of Dark Command
(Death Knight) Glyph of Disease
(Death Knight) Glyph of Icebound Fortitude
(Death Knight) Glyph of Unholy Blight
(Druid) Glyph of Rapid Rejuvenation
(Druid) Glyph of Survival Instincts
(Hunter) Glyph of Volley
(Hunter) Glyph of Possessed Strength
(Mage) Glyph of Arcane Explosion
(Mage) Glyph of Fire Blast
(Mage) Glyph of Fire Ward
(Mage) Glyph of Mana Gem
(Mage) Glyph of Scorch
(Warlock) Glyph of Siphon Life
(Warrior) Glyph of Barbaric Insults
(Warrior) Glyph of Last Stand
(Warrior) Glyph of Taunt
The removed glyphs turn into "Charred Glyphs" which are vendor trash greys. I would definitely recommend getting rid of all the ones in this category that you have piled up via the AH while you still can.
* It's confusing, but the old Glyph of Living Bomb is turning into Glyph of Slow. There is a NEW Glyph of Living Bomb being added that you can learn via Major Inscription Research.