The Nether is once more online. The clean up went smoothly. All chunk data files were pristine and required no updating. Nothing has changed as far as data/items are concerned. I did clean up many old extraneous files from mcMMO, Spout, etc. reducing the total file count from 40,000+ to 248 
Go figure why they were there in the first place. At least the server shouldn’t be straining anymore when trying to find files.
I’m not sure if this will improve the Nether lag – certainly can’t hurt – Even on our local test server, the Nether did still lag occasionally. Time will tell if there is a general improvement.
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Thank you Frelling (: youdabest.