mongo 3.6 replication and write concern timed out
"waiting for replication timed out"  is not a Error , this is a warning msg that your document has not been written to majority of your replica server. but this going to be replicate.

what you can do is along with W:majority configure one more parameter wtimeout:5000 , with this you can overcome of this warning messages.

""Do i just capture it and continue on? or do I need to reprocess some records?""
You can set w:1 for specific process for example a bulk write.