Found this in the faq. The answer is that the funding can be used anytime, even after discovering that there is a reckoning phase, as long as the reckoning effect of either card has not yet begun being resolves (i.e. the card hasn't been flipped).
Q. When can an investigator discard a Debt Condition with a Funding Condition?
A. If an investigator would gain a Debt Condition and he already has a Funding Condition, he may discard the Funding Condition instead of gaining the Debt Condition.
If an investigator has both a Debt Condition and a Funding Condition, he may discard both cards at any time so long as the effect of neither Condition is currently being resolved.
For instance, a Mythos card instructs investigators to resolve reckoning effects; an investigator may choose to discard both Conditions before resolving the reckoning effect of either Condition, but he cannot begin resolving his Debt Condition, decide he doesn’t like what he sees, and then discard both Conditions before finishing the effect.