Lesser restoration does not say it is limited to curing diseases not caused by magic therefore it will cure any disease magical or otherwise.
I also do not think there is a differentiation between magical and natural diseases and it there were there is no reason to belirve chaos phage is magical, getting bitten my a mosquito can result in you getting maleria, getting bittern my a rabid dog can give you rabies but neither of those are magical.
If a DM wants to home brew that a disease can not be cured by lesser restoration they would need to make clear to the players how it can be cured. A Paladin's lay on hand's has essentially the same wording and greater restoration does not cure diseases. Spells like Heroes feast and heal cure any disease the target may have (rather than a single disease) so that could be a differential but they are only available to high level characters.
Can Chaos Phage be remove using Lesser Restoration? Thus Lesser Restoration can cure any magical disease?
Lesser restoration does not say it is limited to curing diseases not caused by magic therefore it will cure any disease magical or otherwise.
I also do not think there is a differentiation between magical and natural diseases and it there were there is no reason to belirve chaos phage is magical, getting bitten my a mosquito can result in you getting maleria, getting bittern my a rabid dog can give you rabies but neither of those are magical.
If a DM wants to home brew that a disease can not be cured by lesser restoration they would need to make clear to the players how it can be cured. A Paladin's lay on hand's has essentially the same wording and greater restoration does not cure diseases. Spells like Heroes feast and heal cure any disease the target may have (rather than a single disease) so that could be a differential but they are only available to high level characters.
Unless the disease says it has to be cured a certain way, then yes lesser restoration will cure it.