Hello!

As in the title, this message came up on the dash. Here's praying its nothing serious. Car seemed to drive as normal. Fault reset after engine restart. Also fault reset after I switched to manual mode and switched back to full auto.

The lights on the gearstick were flickering somewhat and the red 'D' light was turning on and off. Any ideas?

Many thanks.

Welcome!
Assume this is Powershift, if not, ignore!
Initially this is a new, never been seen (by me!) problem, a wiring fault external would be my thought (if internal it's a much bigger problem).
The fact that it is different from auto to manual is a bit suspicious as the auto is selected inside the box via the cable.
The manual is driven by a separate electrical circuit from the gear lever via the wiring loom.
I'd use Forscan with an approved lead and monitor the parameters in the TCM such as Tip+ Tip- etc to see if the transmission is getting a reliable signal.
Also any fault codes when the problem occurs (if you switch off and they reset. that's no good!)
Need to rule out everything external first (what is history and has it had regular oil and filter changes)
On You Tube there used to be a "SK Diagnostics"? (Skoda Yoda?) who had excellent videos including one showing the wiring issue under the wheel arch that stopped the transmission working at all but I just can't find him - anyone?

Battery "State Of Charge" would be my first thing to check.

I agree about battery charge and condition being vital and needing checking as first line but I've never (!) had any gearbox issues related to poor batteries and I've had several of those.
Do carry out that check first, let us know battery age and condition, SoC etc and if correcting that fixes it and make sure to do things one at a time (ideally keeping a record for yourself and us!)