Windscreen drain flap valves missing and gearbox fault

Hi folks, I have a 2011 GP with semi-auto gearbox. There has been an intermittent warning light for a gearbox fault showing up over the past while, always goes away though. Brought it to the dealer and they said it needs about 5 grands worth of work. Local backstreet garage ran diagnostics too and found fault 5FF which seems to be linked to water in the BSI. Also realised today that the fault usually appears when it's raining. I went to check the flap valves for the windscreen drains behind the wheel arches to see if they were blocked and found they were gone! I didn't remove them, and they were there a few years back, so the dealer removed them at some point during a service. So, two questions...is it a problem that these valves/tubes are missing entirely, and could this lead to spurious warning lights?
(sub-question: is my local dealer a crook?)
Thanks in advance!