It'll still be 0ppm whether you're flushing or not mate
Resin is designed to get you 0ppm whether you're putting 300ppm into it or 6ppm
By putting a lower ingoing TDS though, you are prolonging the life of your resin as it 'does't have to work as hard to filter the water'(it's not quite as literal as that but it's the best way to describe it!)
So...when flushing, you'll be putting a higher TDS through your resin (albeit not a lot) so you'll still get 000ppm, you'll just use a bit more resin to get to 0 then you would if you have your tap set to pure
The best way to check and see the difference is disconnect the DI. Test the TDS of the water that would normally go in to the DI when your RO is set to flush, and then when its set to produce. That will then show you what TDS you are putting through your resin
Like I said, the amount is negligible but it cant do any harm to disconnect whilst flushing (I always have on my 4040)