Short answer: yes. Ordnance officers in St. Louis contracted with Miles Greenwood of Cincinnati and E.K. Tryon of Philadelphia to convert 20,000 Austrian tubelock muskets for General Fremont in September 1861. (Congressional Serial Set #1136, p.109, Joint Committee Report, pp 46-7).On October 15, 1861, Brigadier General Sherman contracted with Greenwood "for rifling and percussioning U.S. muskets"; most likely flintlocks seized from rebels in Kentucky. (RG 156, E5, Vol. 13, p.457, Letters to Sec'y of War).
Absolutely. The Federal Government had no less than 45,023 musket altered between 1861 and 1863 with the last delivery of altered muskets being made by Henry Leman on May 29, 1863. Northern States also contracted for the alteration of flintlock muskets and rifles during the same time frame and in excess of 50,000 longarms were percussioned for the States; mainly New York, New Jersey, Pennsylvania, and Ohio.
The alteration figures are a bit squirrely since some numbers of cone-in-barrel altered muskets were re-altered with chambered breech pieces between 1861 and 1863, and records don't usually differentiate between guns altered from flintlock or guns realtered from cone-in-barrel alterations.
The Confederacy and the States that composed it also altered flintlock arms to percussion during the war. There isn't a readily available figure of the number of arms percussion altered in the South, but if I was pressed to give a quick ballpark estimation I would put it in the 200,000 gun range. Limited domestic manufacturing capabilities made the use of percussion altered muskets even more necessary in the South, and Confederate ordnance officers did not hesitate to percussion altered anything they could get their hands on including some leftover arms from the Revolutionary War.
This is an example of just how far back they went when doing conversions. I wish I owned this, but it is just a photo from an auction. A Springfield musket conversion that was originally made before they even started putting dates on the lockplate, with the very earliest style of markings. The buttplate tang is dated 1800, meaning it was about 62 years old when it was converted!
Many had been converted before the war. When the Ohio National Guard was formed in 1864, The Ohio Arsenal was practically empty ( the guns the state did have were sent into federal service and not returned). They were able to obtain obsolete arms from the US Government for the ONG, many of these were converted flintlocks.
At Stones River, 60% of Confederate Infantry was armed with smoothbores. Union smoothbores were about 40%. I am not aware of any flintlocks, so it is likely that the majority of the smoothbores were conversions. With the exception of the Mexican War, th U.S. hadn't fought a hot war since the War of 1812. Militias in most states had been stood down soon after. A Florida regiment at Stones River made an attack armed with muskets so decrepit that many carried the hammer in their pocket. Rear ranks carried sticks. They suffered over 80% KIA attacking the Round Forrest on Dec. 31, 1862. Goes to show, there was something worse than being armed with a .69 cal. Tower of London Brown Bess.
In answering the original question the answer is yes; highly probable but not conclusive (Kentucky). It has been mentioned in early documentation that Ohio contracted with Miles Greenwood to alter and rifle flintlock muskets. As of today I haven't found any clear or conclusive documentation / evidence to this assertion. It's true that Greenwood contracted, likely under an agreement with Ohio, to rifle and sight a number of US altered muskets; muskets that had already been converted from flintlock to percussion - including the M1842. It's questionable, however, knowing the number actually sighted but that's another story.
Miles Greenwood had several contracts in 1861 with states like Ohio, Indiana, and Kentucky but only provided parts (musket) to the latter and cannon to the other. As some of you may know Greenwood had several contracts for cannon. As for altering and rifling muskets in the latter part of 1861; when speaking of those in Kentucky - my own assumption - is that the arms altered and rifled by Greenwood were those sent by the general government to Louisville to arm an Indiana regiment. Much to the surprise of those who opened the boxes saw flintlocks instead of altered muskets. These were purportedly never issued and were retained. Eventually, so it appears, the Indiana regiment received Enfields. Prior to this they had originally received Belgian arms. Complaining to the governor of Indiana they ended up with the Enfield muskets. There are records found in period newspapers describing how some arsenals were altering arms in early 1861. It can only be assumed that these arms were those flintlocks left in storage that had never been altered. The term altering is also elusive because in some cases it may only refer to an arm that was rifled rather than altered from flintlock to percussion. My two cents of course and other opinions will very.