Youy are right: record keeping for an army at war is very much a daunting task at any time in history. During the Civil War, for example, men would routinely appear and then disappear and reappear on the muster rolls. Old soldiers were especially good at allegedly going on detached service and falling off the map for extended periods of time and, when the shooting stopped, reappear.
I can't speak for the other regular regiments, but have found the records for the 1st Dragoons to be fairly well kept. Of import, it should be noted that your figures for desertion date from 1848. The last troops did not leave Mexico, if my memory serves me right, until July of 1848. Several regiments headed to New Mexico and California directly from Mexico. This meant that the figures initially posted in 1848 were the product of much guess work. It wasn't until 1849 that the adjutant general was able to get a handle on the varying reports and make sense out of them. Unfortunately, several generations of historians have used the 1848 reports and overlooked the 1849 AG report.
Post-Mexican War desertions were epidemic, especially out west. Virtually the entire rank and file of the Mounted Rifle regiment deserted en masse once the regiment reached Oregon in 1849. During the same period, Companies C and A of the 1st Dragoons and Sherman's 3d Arty. were steadily losing men leaving for the gold fields. Department of the Pacific ultimately ended up granting lengthy furloughs to allow the enlisted men an opportunity to search for gold.
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