Based on Sanhedrin 18a,1 many commentators interpret "שרי אלפים" (when used in the Chumash) to refer to officers who were each appointed over 1,000 men (including Rashi, Sh'mos 18:21; Tosafos Sanhedrin 18a, s.v. נמצאו; Rabbeinu B'chaye, D'varim 1:15; Ramban, B'midbar 25:5).
It is possible that these opinions would concede that "שרי אלפים" eventually became a vestigial title referring to generals who commanded far more than 1,000 troops, and it carries this expanded meaning in passages about the era of later kings such as Y'hoshaphat.2
Nevertheless, there are commentators who understand the term "שרי אלפים" (as used in the Chumash) to denote a meaning more consonant with the passage in Divrei HaYamim, in which case no reconciliation is required:
The Ibn Ezra (Sh'mos 18:21) proposes that there were only a few שרי אלפים, perhaps the twelve heads of the tribes. Each officer was so titled, the Ibn Ezra suggests, for having 1,000 attendants and aides-de-camp.
R' Eliezer Ashkenazi (Ma'asei HaShem, מעשי תורה, ch. 5) rejects this suggestion of the Ibn Ezra, and instead argues that "שרי אלפים" is a broad category of senior officer including those who were basic שרי אלפים, commanding 1,000 men each (roughly equivalent to a modern day colonel), and extending up to the שרי מאות, who each presided over 100,000 men. Accordingly, the top generals listed in II Divrei HaYamim 17 were שרי אלפים, but they were in the upper echelon thereof.
1 "תנו רבנן ושמת עליהם שרי אלפים שרי מאות שרי חמשים ושרי עשרות שרי אלפים שש מאות שרי מאות ששת אלפים שרי חמשים שנים עשר אלף שרי עשרות ששת ריבוא נמצאו דייני ישראל שבעת ריבוא ושמונת אלפים ושש מאות"
2 See M'tzudas David who appears to provide two different interpretations for the term "שרי אלפים" when used in II Divrei HaYamim 17:14 and in 25:5. In the former case, he interprets it to mean "officers over camps of thousands", perhaps suggesting that such an officer could command many thousands. In the latter case, however, he indicates that each such officer commanded 1,000 troops. This may suggest that the term can carry various meanings even in later usage.
Also see Ralbag (ad loc., 17:14), who points out that the army expanded dramatically under Y'hoshaphat's reign. Perhaps, then, an alternative explanation could be that the five generals described in II Divrei HaYamim 17 were previously commanders over only 1,000 troops each but were then promoted to lead the army under Y'hoshaphat's military reorganization.