I have duplicated the same sample for three octaves, adjusted the keyrange so that it plays like if you drag one sample in and don’t set it to drumkit where it is repitched for each note. I have done this so I can finetune individual notes in the scale for microtonality. Now the filesize of my project has gone from 18mbs to 350mbs. I have checked the xrns file in winrar, and it has 36 exact duplicates of the same sample. This is ridiculous as it’s a waste of space and it takes forever to save. How can I make renoise use one single flac sample for all of the duplicates?
As long as you need individual sample settings for each sample, you need a unique copy of the sample for each one.
The ability to alias samples went away with 3.0, for a number of reasons.
And yes - it sucks from a memory, disk consumption point of view, but made the user interface and general instrument model/API a lot more simple to work with.
I think everyone agrees that the ability to alias sample data is a great one, and it might be re-introduced - albeit in a different form (one which operate strictly on the sample buffer, not the sample level)
Edit: and of course, I’d personally like to see a key-tracking modulation device that could affect notes on an individual level. That would be a completely alternative and lightweight solution to what you are trying to achieve 
But the actual flac audio files are totally the same, there’s no difference between them whatsoever, they’re just a load of duplicates. The only reason I did that was to be able to microtune each note of the scale. Why does it need there to be duplicates when they’re not actually saved as anything different?