I pretty much eliminated the misfiling problem when I put the transcribed Arkansas service records into a database and was able to cross-reference everything. And the War Department clerks had the prison camp rolls to work from, so most men who entered the POW system had a record. However, and I think your advice really hits the mark here, most of the men who were paroled by commanders in the field have no record of it in their Compiled Service Records, because those parole records were not available to the clerks. The only significant exception is that special cartel that Sherman and Hood worked out in September 1864 -- those men are all documented.
The lists of prisoners paroled in the field are surely sitting around somewhere, perhaps in the unfiled papers you referred to, but I've never been able to track them down.
All of which leads me to believe that the 17th Arkansas men captured at Bentonville in February 1862 were paroled in the field.
Your comment about misfiling brings up an interesting point that other Arkansas researchers might be interested in. When I transcribed the rolls and prison records of Dawson's 19th Arkansas Regiment, I ended up with quite a few men who were captured at Arkansas Post and admitted to Federal prisons as members of the 19th Arkansas -- yet they do not appear on the rolls of Dawson's regiment. I was stumped until by accident I happened to come across the rolls of the 19th Texas Regiment -- also captured at Arkansas Post at the same time -- and lo and behold all my mystery men were listed. Apparently, when some of the 19th Texas men were loaded aboard transports to take them to prison in the North, they were misidentified as belonging to the 19th Arkansas.
Many of the these men are included on the 19th Arkansas "miscellaneous" page on the Gerdes site.