OK I just got out of the first dungeon, I went to the seven vales inn and fought these guys and afterwards my familiar is hostile! I go to rest, I even do some other quests. It remains in the inn hostile to me!

Did you hit it with "friendly fire" like some sort of area of effect spell? You might need to reload to a point just before that battle.

I find that, in general, it is better to keep the familiar in your backpack to avoid their untimely demise. There may be some circumstances in which you send the familiar out (scouting or some type of defensive spells) but they really don't have enough hit points to last long in battle.

Just in case you don't know, you can click on your familiar to talk to it and then choose the dialog that lets you put it in your pack.

Maybe it's mad that you didn't feed it. Just stop by the Adventurer's Mart and pick up some familiar food.

Or reload and make sure you're patched. Either way should work.

If I remember correctly, one of the men at the Seven Vales Inn (a wizard) has with him his familiar, an Imp named Pooky. Go and check if that is the case, if it is, it was never your familiar to begin with, but an enemy who probably went invisible at the beginning of the battle and evaded your sight. Hope thats the case,
-Brainless One

This could be the case, though it probably was an area affect spell of some sort. What is your Class/Alignment?

Neutral evil

Its not pooky its a Dust mephit. Its hostile but it wont attack me

have you tried killing it and seeing if you loose the point of CON?

have you tried talking it into you pack?

i suppose you could kill it, take the CON hit, put it back up with shadowkeeper, then recast the spell

some thoughts anyway

can you actually leave your familiar somewhere and move to other areas - i'd have thought i'd have heard about that as a way of freeing up an inventory slot and keeping the 15HP

doom - greater malison - dire charm/dominate

should solve your problem if it is indeed your familiar

If you have cheats activated, you could try and CTRL+Q it into your party (assuming you have space) and then that should make it non-hostile. Talk to it and make it enter your pack. Assuming nothing is messed up from then on, that may work.
-Brainless One