First, let's get the obvious out of the way. Have you tried to restore the ability by resting? I will assume that you have tried and that it doesn't work.
I would think the first obvious issue would be to make sure you have enough levels of ranger to even summon the companion.
I used to play on a server with this exact class combination so there must be some other issue at work here. Yes, you can only summon your companion once per day and your shadow once per day, but the only effect this should have is that one will negate the other if the other is present already because the game engine only allows one companion to exist at a time. If My wolf was running around with me and I used summon shadow, the wolf disappeared.
That negates possibility one.
Possibility 2:
You have two Summon Companion feats, but only the one from the most recently leveled class is usable... Personally, I would rate this as unlikely, but a simple test would tell for sure.
You answered this one yourself. This is not how it works, nor does...
Possibility 3:
The shadow has permanently replaced your pet. As a pessimist, I would say this is just the type of high-handed behavior to expect from a developer.
Fortunately the developer wasn't as high-handed as you expected.
I suppose the bigger question would be where this is occuring. Is this vanilla NWN? Is this occuring on a multiiplayer server? Have there been script changes implemented either on a server or in a module that is triggering the issue? A bit more information is needed to really start making considerations.