Interesting mystery. The key would be to learn what specific action could be tied to his original bond. It seems unlikely that he could have made it to the MSG to enlist in the march time frame (being North of Missouri River.) So perhaps he was operating with some local guerrillas or just trying to work his way south when captured in March (or before.)
If he paid a $1000 bond, then it indicates something more than a simple oath for the privilege of voting, doesn't it? Wouldn't it indicate he was captured or held for some perceived offense and/or taking up arms as stated?
It seems likely that he was first rounded up early on during suspected guerrilla war/recruitment efforts in the area, but prior to the recruiting expeditions following Pea Ridge. He would have still been in his home area during the time of Pea Ridge based on the bond. A few months later Porter was actively recruiting in the area, there was the battle of Kirksville, etc. At that time he again attempted to join the MSG but was again captured, and this time it would be a capital offense.
I don't see why Gen. Merrill who was head of the St. Louis Division that encompassed the fight at Moore's Mill would have been unable to learn if the person had violated his oath/bond. The unfortunate would have been recorded as a prisoner somewhere, given an oath/paid a bond, and released.
The fight at Moore's Mill occurred on July 28, 1862. If he had enlisted the day before (as stated), does that indicate that he might have been captured there? If not he was probably captured with ~250 others at the battle of Kirksville on August 6th. Either way, there was plenty of time to check with other authorities before determining his fate.