Ryan, I don't think the calculator is the issue, because the 2025 VFCP doesn't measure against plan performance at all.
For delinquent participant contributions, section 7.1(a)(2) requires the Principal Amount plus the greater of (A) Lost Earnings or (B) Restoration of Profits "resulting from the employer's use of the Principal Amount" (90 FR 4192, at 4217). Lost Earnings is defined in section 5(b)(6): the 6621(a)(2) underpayment rate for each quarter, applied through the Rev. Proc. 95-17 factors (at 4213). Restoration of Profits is the profit the employer made by using the money, not the plan's return.
So the "greater of" is Lost Earnings against the employer's profit. The underpayment rate is never negative, so a down market in the plan doesn't reduce what VFCP requires. The Online Calculator only does the Lost Earnings side. If the employer actually made money on the withheld amounts, that comparison is yours to document.
Negative actual returns usually come up outside VFCP, when someone corrects under EPCRS on actual earnings. That's a different method, and the DOL calculator isn't the measure there.
Two 2025 changes that do affect the calculator:
Under SCC the Loss Date is the date of withholding, section 5(b)(3)(ii). A full VFCP application uses the date the contribution could reasonably have been segregated, section 7.1(a)(2). The examples under 5(b)(4) show payday on the 1st giving a Loss Date of the 3rd under VFCP but the 1st under SCC. Same deposits, slightly higher number under SCC.
SCC requires the Online Calculator, section 5(b)(6)(vi). A full application can use it or a manual calculation with enough detail to verify the figures.
If it's useful, there's a worked example of that SCC vs. VFCP loss-date difference (three late payrolls across the Q1 to Q2 2026 rate change) at https://401kaudithelp.com/lost-earnings-calculator/. Disclosure: I help maintain that site. The calculator is free