Tax records: I don't think there was a Federal income tax at the time, so you can't dig in the IRS.
Actually, the first Federal income tax was imposed during the Civil War under Article I, section 8, clause 1 of the U.S. Constitution, then again in the 1890s, and again after the Sixteenth Amendment was ratified in 1913.
Just sayin'.
Church records: I'm not entirely sure how organized Protestant churches were at that time; today, the various denominational conventions would eventually notice they had stopped hearing from this church, but it wouldn't be immediate. I suspect Catholic dioceses disappearing would be noticed somewhat sooner.
While we Catholics outnumber any other single Judeo-Christian denomination in America, we're not the best records keepers AND we're outnumbered by the total number of Protestants.
However, the REAL records keepers among the relgions in the USA are the Mormons. They're so meticulous that many geneological and ancestry searches start with their data.
Military records: There are only so many units available at that time, and there are only so many ships capable of supporting a company- or battalion-sized landing. Look for any odd movement orders that may not have been covered up, particularly rail travel.
I have 3 words for you: redacted, redacted, redacted.
If the military doesn't want you to know, you're not going to find your answer in anything you get from
them.
Atlases: Find old atlases and compare them. Maybe one from 1926 that showed the doomed towns was missed in a library somewhere. See if Rand McNally has an archive. Oooo, Library of Congress!
Just a word of caution here: commercial map companies often include bogus data in order to keep track of copyright infringement.
You may find a city on one map that is absent from another, and go "Aha!" when in reality its nothing but disinformation on the company's part.
(And that may have even been a bit of inspiration for the
Hunter the Vigil book.)
Check out the UFO/conspiracy theory/occult section of your local bookstore or library. There have been many cities whose populations have been "disappeared" over time, for a variety of reasons. That fact was the part of the basis for the Dean Koontz novel (and later, movie)
Phantoms, and Stephen King's
Storm of the Century.
Generally speaking, this area is a fertile ground for speculation for all kinds of writers.