Yes, I'm remembering you. Nice to know your research is ongoing. Please let us know what you turn up.
Regarding the discharging of the extraneous men from the Missouri State Militia, I have never done any in-depth research on exact timelines, or even when the individual units were informed that this was going to happen. And technically, the 12th MSM didn't become the 5th MSM--the 5th MSM had already been existing as a unit since late 1861.
Most of the MSM regiments were larger than battalion-size but not really fully staffed up to regiment level strength. The 5th MSM and the 12th MSM fit into this category. So the 12th MSM ceased to exist entirely--poof, gone. Most of its companies were then integrated into the two other regiments, one of which was the 5th MSM, and the other was the 3rd/10th MSM (more on this below).
These MSM companies that moved en masse from one regiment to another generally took on a new company designation letter. So a Company A in one regiment that moved to another might end up being designated Company K. But they were the same companies, just in a different regiment and with a different company designation.
As a footnote, regarding the 3rd/10th MSM Cavalry some of the companies of the 12th consolidated in to--this was not the original 3rd MSM Cavalry formed in December 1861. In the February 1863 restructuring, the 3rd MSM (Old) disbanded, and its troops were discharged or redistributed throughouth the MSM structure.
So....shifting back to the 12th MSM--as discussed, it ceased to exist with some of those companies being integrated directly into the existing 5th MSM Cavalry; the remainder of the 12th MSM was consolidated with the 10th MSM Cavalry, with that reconfigured single new organization then being designated 3rd MSM Cavalry (New).
This is the unit I imagine you are most familiar with. William T. Leeper was captain of Company B, 12th MSM Cavalry, which became Company L, 3rd MSM Cavalry (New). As a Radical Unionist he didn't last long in what was mostly a Pike County Conservative Unionist regiment and was kicked out before year's end. His company was then quickly detached from the 3rd MSM and was sent to cool its heels for the rest of the war on garrison duty in Cape G.