CombatWombat

The cable comes from behind the grey carpet-like trim, over its top edge, directly to the right of the light (viewed from rear bumper). It is easy to forget it needs pulling through when aligning the trim pieces.
 
I don't think it can drop very far down the back of the vertical/carpet panel, that's where it probably is now.
 
The hard plastic panel (with the parcel shelf hinge), that is above it, is more easily removed when the fabric-covered C pillar trim is removed (C pillar trim has 4 spring clips - v. stiff). The hard plastic parcel-shelf-pivot trim has three screws and many clips and an extra screw into the retracting curry hook at the bumper end of the boot.
 
And that is more easily accessed when the rear seat side bolster has been removed. Which needs the rear seat base taking out.
 
There must be an easier way.
 
Perhaps start with the C pillar trim, loosen the screws nearby and see if you can retrieve the connector with a bit of stiff wire down the back?!

Had a similar problem last week with a Mazda. Removed the fan; two small leaves had found their way into the middle of the fan impeller (fan is almost identical to a Skoda one). Removed leaves - problem gone.  Really surprised at how much noise they made, and just as your description.
 
Haven't removed the fan on an Octavia, but have on a Superb, which I think uses the same heater box. It was pretty easy, as long as you don't mind laying on your back over the passenger door sill. It sits behind the glovebox. The power connector has two small 'wings', one at each end, which need squeezing to release it. Then, the motor rotates about 1/8 of a turn after a plastic tang has been lifted/disengaged. The motor drops down, provided the carpet/wiring loom/soundproofing isn't too close.
 
It's probably more fiddly to get back in. The locking tang slides up a ramp on the plastic housing, (on the casing that stays with the car), as the motor is twisted in the opposite direction.