Metabolome Pathway Analysis

Hi There,
If the PLSDA permutation test fails, should we include the metabolites with a VIP value above one in the Metabolome Pathway Analysis and Set Enrichment Analysis? Can we trust the pathway results when we have already included metabolites that failed the permutation test? If not, what is the solution? How can we perform pathway analysis for data that failed the permutation test?
Thank you so much in advance for your time and help.