I had 2 Glass Bows at Legendary level - one did 90 damage and the other 96 (because I used a Fortify Smithing potion when I smithed the 2nd bow.)

I had one Grand Soul Gem so I selected the 90 Damage Bow and Shock enchantment and watched the base damage drop to 47!

So I switched to the 96 Bow and same enchantment and gem - no drop in base damage.

So what gives? Why would one lose a huge chunk of damage just because I enchanted it?

Its not a stolen item (not that that should make a difference). I have the Arcane Blacksmith perk.
Is this just another bug? Perhaps its the beta patch (which I'm using btw).

It says the damage goes down, but it really does not. Once your done encahnting it will have its smithed damage.

The game doesn't take smithing improvements into account when it gives you that number. It will go back to the original damage after you enchant it.

i have an enchanted ebony greatsword . i know it did either 97 or 104 base damage and i have had it for a while. all of a sudden i noticed it only does 66 base damage now. enchanments stayed the same.

66 would be if it was not improved. Or, somehow your weapons skill is damaged and that is why it is lower. Go get healed.

Are you wearing different gear? The number on the inventory screen is the actual damage depending on your skill, perks, and all enchantments on your gear.

So why does one bow go down and the other doesnt?

If you are using the beta patch it sounds like the sort of thing to write out in detail and submit as a bug report.

Pretty sure you removed or replaced some gear with +damage, common if you have combat and smithing or alchemy gear.