Does the paper texture affect the final Canvas print? would it clash with the actual grains in the canvas?
I applied it through "Effects > Apply Surface Texture".
Is there a way to remove it from the .rif file?
it's hard to answer your question without seeing an example of what you currently have and what you're planning to print this on.
generally speaking if you are adding very pronounced, rough paper texture it will probably look off if printed on heavily textured print medium. painter's "apply surface texture" tool fakes texture variation for artwork presented on screen, or printed on basic flat paper to create illusion of light hitting a grainy surface.
if you are printing on an actual artists canvas and have a medium to light texture treatment done in painter it might be not very noticeable.
if you don't have a pre-texturized canvas saved as a separate document, you won't be able to remove the paper grain - it's baked in.
you can potentially remove some of it by either over-painting again, or doing color correction. maybe throwing a blur effect and painting over would remove some of that.
Any pixel that its affected byt the paper texture it will print the same. Will it add fake texture to places that brushes with no grain were used?....No.