I have almost the exact same problem, which came about this afternoon when I changed the battery in my 2009 (LDH) Yeti TDi 4*4 2.0...

I now can only get into 3rd and 4th; the problem is that I can't logically link this problem - which seems inherently mechanical in nature - with the removal and replacement of the battery.

The gear lever can be pushed to the appropriate position, but the relevant gear does not engage and the lever drops back to a non-engaged position.

All the lekky bits work fine.

Anybody know if this is a known problem with an easy fix?

The clutch smells every time I pull away in 3rd, and I can't drive everywhere at 80 kmh maximum at 2500rpm 

This post has been moved here to hopefully get more relevant assistance than where it initially was.

You didn't drop a tool (for example a spanner) down the back of the engine?

as above I would check you haven't left something near the gearbox linkages that is preventing you getting into 1st and 2nd