I am currently reconditioning a set of 's' discs. The faces of the drive flanges which push on the back of the outer bearing have wear marks in them from obvious bearing failure/ lack of tension on the driveshaft nut. New ones cost around $100 so im not too keen on buying new ones unless i have to.
Is it possible to machine the thrust face or will this bring the rotor in too far?

cheers, chris

Before you even think of that try putting them on an unworn part of the CV's spline and rocking them about. If loose, I'd chuck them.
Also look for wear on the splines of the CV.

Machining a few thou off to clean up won't hurt, but they MUST be set up accurately in the lathe with a dial gauge on the disc mounting face.

Hint.. if you need new drive flanges it's cheaper to bring these in from MiniSpares UK than to buy them here...

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DrMini- 1970 wasaMatic 1360, Mk1S crank, 86.6HP (ATW) =~125 @ crank, 45 Dellorto (38 chokes), RE282 sprint cam, 1.5 rockers, 11.0:1 C/R.

is that the same as minidirectaus?

yup, anything bought from minidirectaus actually comes from MiniSpares in the UK, minidirectaus just has the pricing in AUD.