The official 28th NY history mentions the loss of the colors at Cedar Mountain but only to elaborate on the circumstances of the return of the National flag (pictured in the article to which you linked) not a Regimental flag. The National flag which was captured at Cedar Mountain had no markings on it to identify it as being 28th NY and it was only identified as a result of a small section cut from the center after it had been captured. This small section of the flag was returned to the regiments Colonel (Edwin Brown) after the person who took that piece was released from Libby a few months later.
This flag was recaptured when Richmond fell and was placed in the Flag Room in Washington where it hung until Colonel Edwin Brown saw it, identified it by the section of the flag which he still kept with him, and invited the 5th Va to officially return it in 1883. It was the first joint reunion by a Union and Confederate regiment after the war.
You mention that in "Stonewall Jackson At Cedar Mountain" it states that the 28th NY regimental flag was captured and another unidentified flag. As the national flag of the 28th New York was not marked to indicate it as such, I'd suggest that the unidentified flag could be the National flag of the 28th which was also captured at Cedar Mountain and returned by the 5th Va in 1883.
Thanks,
Simon Taylor