Data filtering and NAs vs Zeros

Hi! I’ve been using metaboanalyst statistical analysis for analyzing a large untargeted metabolomics dataset. As usual, there are 0 values (which are not necessarily zero, just below the detection limit). I am confused if I should be replacing these with NA now? In past versions, I’ve tested both and it yielded the same results (because I believe at the time it was just replacing both with 1/5 of the minimum value). Because of that, I stopped bothering to replace the zeros with NA, but it has come to my attention that MetaboAnalyst now offers different options for dealing with NAs vs zeros. For zeros, it seems to continue to just replace them with 1/5 of the minimum value, but if you select this option when plugging in NAs (which, in theory, should give you the same results), it gives you different results. I’m unsure which one I should be using, and any advice would be much appreciated!