How can I find out if my gene of interest is duplicated?
You might want to have a look at What is the difference between orthologs, paralogs and homologs?. Paralogs are duplicates by definition, and whether a gene is a pseudogene or still active has no bearing on whether it comes from a duplication. 

In any case, to figure out what's going in in your target genome, you should use the target's genes. So, first get the best hit for each of your query genes in the target genome. Then, to investigate its evolutionary history, use that sequence (the one from the target genome) as  query against the target genome. That will let you assess how similar the target's hits are to one another and that's how you can attempt to figure out their evolutionary history. 

Note that 20% identity is very low for closely related species. While there is no golden threshold, I would expect recent duplication events (and in closely related species, a duplication event that is in one genome and not the other will be recent) to produce much more similar sequences. In any case, you can't do this based on sequence identity alone. 

Are the protein domains of the gene products conserved? Is the exonic structure of the gene conserved? You should also try taking the putative duplicate of geneA from genome2 and blast it against genome1 (your original source genome). Is the best hit the geneA from genome1, the query you used to find the putative duplicate in genome2? Or is there a better hit for it against another gene? 

These are all questions to investigate and take into account when reconstructing the evolutionary history. You can't just look at identity and use some threshold to decide this sort of thing.

If you blast the potential dupicate from your target genome against your original source genome, is the best hit the duplicate?