The issue of constant targeting—that is, if an effect present on a creature, object, or area is always confirming or denying if the target is valid and, if denied, something happening (dispelling, suppressing, exploding, etc.) to that target or effect—is unmentioned, so far as I'm aware, anywhere as a general rule. (Specific effects may mention constant targeting, but, for example, a familiar's share spells ability doesn't nor does the 3rd-level Sor/Wiz spell primal form [trans] (Spell Compendium 161).)
The D&D Main FAQ—with which some folks take issue—addresses this idea, albeit obliquely:
If, while under the effect of a spell that depends on type (such as hold person), my character is transformed into a different creature type by polymorph, does the spell’s effect remain?
Yes. A spell only checks to see if you are a legal target when it is cast. If you become an illegal target later (such as via the polymorph spell), the spell remains in effect. (87)
(I am unaware of this question's provenance.) With nothing from the rules saying constant targeting is a thing and this ruling that—for this specific case, anyway—it isn't a thing, this DM feels comfortable ruling that if an effect's target was legal when the effect was activated, then the effect continues even if the target later becomes illegal.
In short, this DM—like yours—would also rule that the familiar continues to benefit from the shared spell, even if the familiar no longer possessed the ability share spells after having received the shared spell.
