If that is so, then where to the numbers suggesting about 500 POW's come from, and how come only 50 or 100 or whatever it was went to San Antonio, the rest going to Illinois?
They are a commonly cited source which contain both the available Union and Confederate papers.
Indeed they are, but they're also replete with low level officers embellishing their accomplishments on the battlefield. Your account of Sibley appears to be one such embellishment as it presumes substantial amounts of information WRT motives and what the confederates may have been thinking when the fact is that their troops hardly ever even met each other on the battlefield.
The O.R. account documents a group of approximately 25 sick and wounded taken as pow's when the federal vanguard entered El Paso. They were escorted to San Antonio, on parole, within a week to ten days. Another group gathered of about 100 at Fort Bliss, El Paso, and were similarly sent east on parole two weeks later (this group was given arms for their own protection from "Mexicans and Indians"). There were others taken prisoner throughout the theater of operations, from present-day Arizona, New Mexico, Colorado, and from western Texas. This may even include pow's taken in the panhandle area of Texas and the Indian Territory, and Kansas (the records in the "Pacific" chapters of the O.R. only mention these areas in passing, as they were not part of the Department of the Pacific or the Department of New Mexico).
Account suggest that of Sibley's and Hunter's combined forces in New Mexico Territory, about 500 died from combat or illness, and about 500 were taken captive and sent to Illinois. The rest retreated to San Antonio, or were paroled there. It is also possible some deserted to Mexico.
Your account of Sibley appears to be one such embellishment as it presumes substantial amounts of information ...
My account is based on my reading of the O.R. and Hunt's book on the Army of the Pacific. It has been supplemented by recent web searches, and of course, the documentation provided by rustbucket and others. It actually has been an interesting exercise, because so little is published about the War in the Southwest.
I had never heard of the skirmish at Grinnell's Ranch, Arizona. Apparently it is the farthest west action in the WBTS, taking place between Carleton's California scouts and Hunter's Texans. This was followed shortly thereafter by the Battle of Pacacho Pass, near Tucson.
http://wtj.com/articles/picacho/
I am sure you have better resources concerning the confederate documentation of the actions in the west. You are welcome to post them.
Here is another passage which bears light on the pow count. From Hunt's book, pg 66-67:
"After the Battle of Apache Canyon, a 48-hour truce was declared to bury the dead and remove the wounded. Sibley and his Confederates troops retreated to Santa Fe and the Colorado volunteers joined General Canby's command and pursued the Southerners down the Rio Grande river.
"Sibley's brigade was a two-day march ahead of the Union forces and by the second night had reached Peralta. The confederates followed down the west bank of the river, while the Union troops occupied the east side; both armies were in full view of each other, the river alone intervening.
"Sibley planned to reach Fort Craig ahead of the Union troops, but the latter were so close upon his heels that he (Sibley) decided to go around the fort. He abandoned his wagons and heavy artillery, and with seven days rations on mules, his entire force struck out after dark on the hazardous route through the hills. They succeeded in reaching Dona Ana safely and proceeded across the border to Fort Bliss.
"They were not able to move their sick or wounded, so left them at Santa Fe, Albquerque and Socorro. Mrs. Canby and the wives of other Union officers cared for these soldiers for several months, as it was not until the arrival of the column from California that the last patient and captured soldier was escorted to San Antonio."
Hunt cites the O.R., Ser. I, Vol IX, pg 506-512, 583; (Sibley's report of the battle of Valverde, etc.).