Okay, I have it figured out, thanks to Tom's find in the 1864 Adjutant General's Report. Our guy Isaac Snedicor
never held the rank of major under a specific regiment. In that A.G. Report under the name spelling Isaac D. Snedeker, Snedicor appears not once, but twice, under heading "Paper D -- A Complete Roster of the Staffs." Subhead "Commanders-in-Chief and Their Staffs, Major Generals Commanding and Staffs, and Brigadier Generals Commanding M.S.M., and E.M.M., and Their Staffs, Including and Since the Year 1861."
As indicated by that subheading, the listings of all staff members is divided by individual names of multiple members of the senior command staff starting with Gov. Hamilton Gamble. Now this entire section here indicates these staffers were appointed pursuant to General Order No. 96, U.S. War Dept. I found that specific general order in the Abraham Lincoln Papers, and it was issued November 7, 1861. It is the seminal document giving birth to the Missouri State Militia. So, that tells me most of these staffers, most with field officer ranks, were appointed by the legal authority relating to the Missouri State Militia.
However, below the G.O. 96 staffers, there are also listed "Honorary and E.M.M." staffers. And under the initial section of Paper D relating to Gov. Hamilton Gamble, there's Isaac D. Snedeker listed as "Major and Aid-de-Camp" under "Honorary and E.M.M.," to rank from Feb. 26, 1862. Since the EMM wasn't founded until July of that year, that indicates his rank of Major was honorary. But not just 'sit by your fireplace and pretend you're a soldier honorary.' His honorary rank came with a pit-bull bite, since he was also appointed provost marshal for Callaway, Audrain and Montgomery counties to accompany it.
And, it appears this honorary rank was NEVER rescinded, even when Snedicor got into all the trouble he got into. In the listing for all these dozens of staff members, there is a remarks section for each man. These remarks have a garden variety of comments, including "Died" "Resigned" "Vacated" etc. And in the remarks by a large number of these staffers is the comment "Transferred to staff of Governor Hall."
In essence, when Gamble died, their status changed from being an aid-de-camp to Hamilton Gamble to aid-de-camp to Willard Hall. Thus accounting for Snedeker/Snedicor's second appearance in this "Paper D" listing of command staff members. As noted, the first listing for Snedeker was under Gov. Gamble's section of the listings, with a comment he transferred to staff of Gov. Hall. Now right below Gov. Gamble's staff listings, Gov. Hall's staff listings appear. And, under the "Honorary and E.M.M." section for Gov. Hall there appears Isaac D. Snedeker along with two dozen plus other names. So Conservative Unionist Snedeker never got hit with a "Died" or "Resigned" or "Vacated" comment by his name; he's on the list of Gamble staffers, and then afterward on the list of Hall staffers -- which tells me Snedicor's honorary field officer rank survived throughout the war, at least through the tenure of Gov. Hall.
That rank originally granted by Conservative Unionist Hamilton Gamble very well might not have survived Radical Unionist Thomas Fletcher's ascension to the office in January 1865.