My fabia sometimes works from the remote and sometimes notwhen it does not the puddle lights dont work and the window switches swap over !! Also the boot does not lock or unlockany ideas ?

Comfort control module. Code scan will give precise fault.

Skoda garage can't seem to read any codes from the comfort ECU also it has been connected to a Snap on modus which also will not talk to it ?Could this be because the ECU is faulty ?

can a comfort control ecu be removed from another car (ie secondhand )if this is possible does it have any recoding by main dealer and just to verify ecu positioned near clutch pedal?

They can, provided that the replacement is of the same part number. Coding wise, it's all in the label file in VCDS, you may have to adjust it depending on the number of electric windows and door unlocking options, remote locking fobs will need to adapted to it and yes, it is by the clutch pedal. If they can't communicate with it, check your fuses.