Can untargeted metabolomics detect epigenomic changes such as methylation?
This is a fascinating question, and I spent a fair amount of time looking into it. From what I've been able to find regarding the relationship between metabolics and epigenetics, it seems that metabolites drive epigenetic changes, not the other way around. 
This can be shown quite well by looking at cell differentiation and induced pluripotent stem cells. The epigenetic changes that happen in these processes happen due to the cell's environment. 

However, epigenetic changes cause changes in transcription rates, so it can indirectly influence metabolics. The circadian clock uses this system (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3392647/).
Cell signaling appears to be the most significant cause of metabolic change, though. The aforementioned paper also says this: 


  As most metabolites are not diffusible between mitochondria and
  cytosol/nucleus, accurate determination of the cytoplasmic pool size
  is critical to understand their effects on epigenetic signaling.
  Although attempts have been made, so far the technology to reliably
  measure metabolite concentrations in different cellular compartments
  is lacking.


Which, I'm sorry to say, leads me to believe that there are very few metabolic pathways that have known effects on epigenetic factors.
That said, there are several references in that paper which may put you on a good path forward.