Employee incurs dental expense in December 2008, but not paid until January 2009. Out-of-pocket costs exceed balance in 2008 Limited FSA. Employee has balance in HSA at the end of 2008 (and the full further addition in 2009) and wants to use the HSA to reimburse the out-of-pocket dental expenses that exceeded the amount available in the 2008 Limited FSA.

Further complication is that the company switched from using PayFlex as the 125/HSA third party administrator in 2008 to WageWorks in 2009.

WageWorks has twice denied the claim on the basis that the plan can "only reimburse expenses that are incurred during the coverage period." Prior brochures from PayFlex explicitly state that once the Limited FSA is exhausted that further claims may instead use the HSA balance and the employee relied upon this representation.

Any IRS reference on this question? Suggestions?

Isn't this the purpose of an HSA account anyway? I cannot imagine not approving this claim. I have been in the Section 125 business since 1990 and with HSA's since their inception.
You can use HSA funds to reimburse an expense incurred in another year as long as you had the HSA when the expense was incurred.