Handling harmonic overtones

Using (too) low samplerates on Amiga introduces harmonic overtones. Since there is no kind of interpolation applied, low samplerates will produce harmonic overtones (also referred to as aliasing) with the frequency of half the samplerate used. If for example we use a samplerate of 4000 Hz, then we will hear a harmonic overtone of 2000 Hz when playing the sample. The lower the samplerate, the louder the overtone.
There is no way we can get rid of this. Not when using such low samplerates. The only thing we can do in order to make this overtone less unpleasent to listen to, is to make sure it matches the tone of the actual instrument. We can do this by using a samplerate equal to the tone of frequency multiplied by 2 to the power of n.

If, for example, we're sampling a 110 Hz tone, then we should use a samplerate of 110*2^n Hz, where n is any integer we want, as long as the resulting samplerate is within the supported range. 110*2^6 = 7040 Hz for example. That'll make sure the overtone becomes 3520 Hz, which is exactly 5 octaves higher than the actual instrument - in tune with the instrument tone.

The downside to this method, is that it'll most likely require us to resample all the samples we want to use in the track, to make sure the samplerates of all the samples match eachother. Otherwise it'll most likely be difficult to make all the samples be in tune with each other. Protracker doesn't support any samplerate. It'll "snap" to the nearest supported one. So samples with different samplerate-tables can end up being out of tune without any way of fixing it.

The Amiga does actually offer a filter though, which was made with the very purpose of filtering out higher frequencies aliasing when using lower samplerates. A low-pass filter that can be turned on/off with command E0x in Protracker.
I don't personally find this filter particular useful for reducing harmonic overtones though. Sure, it does reduce the overtone a bit - but everything else is also reduced. And the effect applies for all 4 channels - not just the single channel where the command entered. In other words, it's somewhat the equivalent of covering your ears with your hands - and that's not how we want to listen to music now, is it? Not that it doesn't have its usecases. It's ideal for example in games where the player character goes under water. But that's about it really.