Where did the templar ships go when they left La Rochelle?

Answer 1

According to the documents of the time, there were 18 Templar ships in La Rochelle on the 12th October 1307, but the next day Friday the 13th, when all the Templers were arrested, these ships had disappeared.

Answer 2

It is a small posibility that the templar may have fled either to Scotland or Russia. I have found something interesting on a Russian page about the Knights Templar and I quote :

''In 1307 Yury Danilovich Moskovsky was in Novgorod and together with Novgorod archbishop and all people have met "kaliks" (wanderers - pilgrims), who arrived on 18 "nasadas" (the seaworthy ship). We will notice that Rabelais, the French author of the end XIV has described a seaway to Russian northern ports round Scandinavia. Kaliks have brought "infinite many set of gold treasury, pearls and precious stones", and gave all that to prince Yury, to archbishop and to all people; after then wanderers have complained on "unworthy king of Gaul and the Pope".''

Apart from that it is no secret that most catholic order found a safehaven in Russia when the Roman Catholic Church didn't defend them. The Order of Malta had a period of Russian exile and so did the Jesuits when the Pope agreed to their dismantle.