Merrifield, as I am sure you know, did two articles for Confederate Veteran. One is dated Vol. 24, #12, Page 551-552 and the other is Vol. 16, #11, Page 554,
In both articles he states that the 1st/4th Missouri flag was sent to Chicago and it burned in the great fire there.
I think the OR report has the two flags confused with the unmarked "regimental flag" actually being the HQ flag of the brigade whereas the marked flag was that of the 1st/4th Missouri. I base this on two other flags taken at Nashville, both Mobile Depot pattern flags, that were also claimed in OR reports to be the flags of their respective brigades. One, WD 210, is a Tennessee cavalry regimental color (one of three possible of Bell's Brigade) and the other, taken by the 12th Tennessee Cavalry (US) in their fight with Edmund Rucker and the 12th Tennessee Cavalry (CS) was the regimental flag of the latter regiment.
The HQ flags of Lee's Corps were indeed unmarked and were similar to the system of designating flags used by the Union Army of the Potomac in 1863 - geometric shapes with added colors to designate division and brigades within the division.
It has been my experience that Union OR reports that claim to have captured a divisional or brigade flag actually have no clue whatsoever if that is actually correct. Sometimes they are right - and I have found as many, or more, of them being wrong.
Please also consider that flags taken from one side or the other, unless actually clearly marked with unit designations, when asked for their ID from captured soldiers that they might have lied to the captors to spare their unit the shame of losing colors. You can pretty much count on two hands the number of OR reports that admitted losing colors in the war. The case of the alleged 19th Georgia flag taken at Fredericksburg is a case in point. The flag is an unmarked ANV Second Bunting and all of the Union capture accounts state that it was the 19th Georgia's flag and yet thanks to research I have proven that the flag is that of the 14th Tennessee Infantry of the same brigade who were the next in line to the 19th Georgia. So somehow the Union captors were told by some captured Confederates that it was the flag of the 19th Georgia either intentionally or quite by accident since both units carried the same type of flag.
This is the dilemma for captured and unmarked CS flags.