Anita,
I have some of the information that you seek regarding Syracuse, MO during the Civil War including amount of damage, the various fights or raids and killings in or near Syracuse.

I don't think "the entire town was virtually burned to the ground at one time or another." There may have been some vandalism by Union troops to the village during 1861 like what they did to some villages nearby that were known to house a number of residents sympathetic to the southern cause, as happened to California and Versailles. George Todd with just over 100 riders raided the town on 8 October 1864 and his guerrillas torched the railroad depot and a couple of related railroad structures. The depot fire spread to two nearby houses that also burned to the ground, but that was the extent of the physical damage in Todd's raid. Regular Confederate raiders tore up the railroad somewhat during Shelby's 1863 raid and Price's 1864 raid in order to limit the Federals use of the railroads to send rested troops in pursuit of the raiders, but I am not sure precisely what damage those raiders did to the town. The 1860 census bears out what you said about the large population of railroad related people in Syracuse, and I would imagine a lot of those folks remained there until construction of the Pacific Railroad re-commenced by 1864 past Syracuse and eventually into the Kansas City area by late 1864. I wonder if the presence of lots of railroad people prevented both sides from damaging the town too much early in the war. By about 1862 Union authorities placed troops in garrison in some villages along the length of the railroad to protect it from damage since the few railroads in the state helped the Federals maintain connection to western states and territories. I know nearby Tipton had a Union garrison throughout nearly the entire war, but those troops left temporarily in the face of large southern forces such as during the raids I mentioned above. After the Enrolled Missouri Militia (EMM) program started in summer 1862, some local men of the 43rd EMM watched over Syracuse some of the time, and elements of the Cooper County 52nd EMM had men at nearby Otterville and some 52nd men visited Syracuse on occasion. Syracuse had its own full-time Union garrison during parts of 1864, and I recall from reading that elements of the 4th Cavalry Regiment Missouri State Militia (MSM) garrisoned Syracuse at times that year. If the town had been mostly destroyed, I don't believe Union authorities would make troops stay there.

Regarding war dead buried at Syracuse, I found fighting or killing in town or nearby on 11 August 1862, 14 October 1862, 21 February 1863, late August 1863, 5 October 1863, and 8 October 1864 that involved guerrilla warfare. That doesn't count actions with regular Confederate troops during Shelby's raid in October 1863 and Price's raid in October 1864. I am still looking up detail on these actions, and plan to place another reply in this forum later to help answer your questions about burials of war dead in or near Syracuse. From what little I have seen so far I would say it is possible that as many as 100 combatants could have been buried in or near Syracuse throughout the war. I cannot help with grave locations, but I already have some names for you.

Until later,
Bruce Nichols