Re: Lost Titre de Sejour Card
When I lost my wallet (with the permit), the police gave me a special letter to be given to my commune. There was some fee associated with this.
I don't know about customs, but I've always had to show my permit to the immigration when re-entering Switzerland (except for the very first time- it was a Visa D) via the airports. Never (so far) by road or rail.
I would suggest that you contact your commune soon to figure out a solution.