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Hi
I have checked the faq on this and can find no entry in ethier the rules faq or codex faq. Can farseers use fortune on their transported squad while being transported in a waveserpent. e.g. farseer and bodyguard both in waveserpent with fortune on them in case of a crash.

No.

From the main rulebook FAQ:

Q. Can psychic powers (like Fear of the Darkness) or
other special rules (Imperial Guard Officers’ Leadership)
and pieces of wargear (like Psychic Hoods) be used
from within vehicles by models that are being
transported?

A. As transported models are not physically on the table,
they cannot do anything (unless differently specified).
The only exception is firing weapons (and using psychic
powers and abilities that replace firing a weapon) from
one of the vehicle’s Fire Point or from an open-topped
transport. On the positive side, transported troops
cannot be targeted by the enemy (the enemy can of
course target their transport, and the passengers may
suffer consequences as a result).