So a lot of known loyalists ended up being kicked out of the EMM due to the zero tolerance of Special Order 126. Case in point -- Lt. Col. Samuel Cox, Unionist Hero Killer of Bloody Bill Anderson. Tagged as being "disloyal." Can you imagine? He received his faux lieutenant colonel's commission in the 33rd EMM in October 1864 -- after the July 4 SO 126 filing deadline. That commission was then legalized by the governor a few weeks later. But then he got caught up in bureaucracy, and was tagged as being "disloyal" and had to rehabilitate that slur against him in the final days of the war.
Even for those getting caught up in a SO 126 bureaucratic morass in the EMM, there were other avenues for loyalist service for those cast out of the EMM due to its onerous terms. Starting in July 1864, probably not coincidentally, the Order 107 militias began forming, followed by the Order 176 and Citizen Guard militias -- none of which were covered by SO 126 requirements. These alternative militias were overseen by local loyalist "Committees of Safety" who could look at these guys on an individual case by case basis (ex. Unionist Capt. David Guitar of Boone County whose false modern-day saga of being tagged a Confederate is related elsewhere on this board, despite his serving in the Union EMM and post-EMM Federal units).
Those alternative militias were formed in later-1864. Also not smothered by SO 126, in 1865 Missouri Militia and Veteran Missouri Militia units then began being formed under General Order 3 and legislative fiat, sweeping up a number of the SO 126 guys who had been purged.