Missing Familiar and Hit Points

Durothil

When importing a character from the final save file, the found familiar from the first game is missing - including the maximum hit points as if it died.

Gallowglass

Yes. It has always worked that way, and I believe it is intended behaviour. Fortunately, however, you don't also suffer the loss of CON which would normally apply if your familiar had been killed.

You must re-cast Find Familiar to get yourself a new familiar. Unless you happen to have it in your spellbook, this means that you'll have to wait until you find a new scroll of FF before you can again have a familiar, and I'm sure that this temporary disadvantage is deliberate.

As a role-playing justification, you can suppose that your captors have in some manner removed your familiar, or that some such thing happened during the time elapsed between BG1 and BG2. (How the forthcoming "Adventure Y" will address this issue will be interesting to see!)