One page further (p. 587), Huehnergard gives as one of the changes from Proto-Semitic to Old Babylonian:
Common Semitic *ḫ and *x̣ merged to ḫ (Huehnergard 2003):
*ḫamisum > ḫamšum ‘five’; *saḫānum > šaḫānum ‘to be warm’;
*x̣apārum > ḫepērum ‘to dig’; *rax̣āṣ́um > raḫāṣ́um ‘to wash’.
The reference is to the author's 'Akkadian ḫ and West Semitic *ḥ'; pp. 102–119 in Leonid Kogan, ed., Studia Semitica; Orientalia: Papers of the Oriental Institute, 3 (Alexander Militarev volume).
The background is that Akkadian lost ḥ (preserved in West Semitic, whence the traditional ḫ/ḥ distinction), and that ḫ corresponds to ḫ in West Semitic, while there are exceptions to this (where ḫ corresponds to ḥ in West Semitic). The numbers are as follows (p. 112):
Akkadian Ø corresponds to West Semitic *ḥ in about 60 examples; there are in addition some 50 examples of Akkadian Ø with a > e, i.e., in which the earlier presence of either Proto-Semitic *ḥ or Proto-Semitic ʕ is likely.
Akkadian ḫ corresponds to West Semitic *ḥ in about 50 examples.
Akkadian ḫ corresponds to West Semitic ḫ in about 90 examples; there are also nearly 200 additional Akkadian roots with ḫ for which no West Semitic cognates are known.
The traditional solution is that Proto-Semitic ḫ stays unaffected, whereas Proto-Semitic *ḥ is dropped in East Semitic. However, the second group, where West Semitic *ḥ corresponds to East Semitic ḫ, is too large for this. In default of a phonological explanation that can predict which instances of *ḥ become Ø and which become ḫ, we must posit a third consonant for this second group (Huehnergard compares this to the situation of ð merging with d in Aramaic but z in Hebrew; cf. Aramaic dkr vs. Hebrew zkr 'remember').
Because this hypothetical consonant merged with ḫ and ḥ it should be a fricative articulated near the velum or pharynx. Most consonants in Proto-Semitic come in a triadic opposition (voiced/voiceless/emphatic), the exceptions being bilabials and velar and pharyngeal fricatives (none of which have emphatics). Because a emphatic pharyngeal fricative is 'unexpected on articulatory grounds' (p. 115), an emphatic velar fricative x̣ is proposed, i.e., IPA [x'].
We then get (p. 116):
- Proto-Semitic ḥ is unaffected in West Semitic but dropped in East Semitic.
- Proto-Semitic ḫ is unaffected throughout.
- Proto-Semitic x̣ becomes ḥ in West Semitic and ḫ in East Semitic.
Is this the mainstream consensus? I can't really comment since I don't work in phonology, but I can say that (1) you are right to be surprised (2003 is pretty recent) and (2) Huehnergard is usually right.