From my experience with DOL audits, they tend to be fairly strict when it comes to the timing of elective deferrals, even for small amounts. Unlike the IRS, which sometimes allows you to rely on correction programs (like the EPCRS) with certain limits, the DOL often expects plan sponsors to correct late contributions back to the date the deferrals should have been made, regardless of statute of limitations.
That said, DOL examiners will usually consider whether the amounts involved are truly de minimis and whether the plan sponsor acted in good faith once the issue was discovered. Since you already corrected the deferrals from 2000 onward and the amounts for 1999 are small, it may be possible to negotiate a resolution that limits the liability or reduces penalties. Having thorough documentation showing your intent to comply and the steps taken to correct the issue helps a lot in these discussions.
In practice, many small companies end up paying the owed contributions for the earliest period if the amounts are minor, but you can often avoid additional penalties if you demonstrate prompt corrective action and cooperation. Essentially, it’s a balance between minimizing administrative burden and satisfying the DOL that you are acting responsibly.
A good approach is to provide a clear explanation of your correction process, the relative size of the 1999 amount, and ask if they would consider this sufficient to close the issue. Often, they will be reasonable if the amounts are small and there’s a documented good-faith effort.