no no no. ouch, the scars still hurt from having had this beaten into me a number of times, I would point out the following.
1. your document says the plan is safe harbor. therefore, failure to fund the safe harbor is a failure to follow the terms of the document. so the plan is still safe harbor, not top heavy. failure to follow the terms of the document is a possible cause for plan disqualification, but that is the purpose of EPCRS.
2. 1.401(k)-3(h)(1) .......safe harbor contributions must be made within 12 months of the end of the plan year. [just like any other QNEC or QMAC.]
so there isn't a Sept 15 deadline, there is a 12-31 deadline.
now, at one of the ASPPA conferences the issue was raised about how this effects the 415 limit (annual additions)
normally you have up to 30 days after the deadline, so 10/15 for a calendar year plan. if contributions are made real late (after 12/31 they are corrective contributions under EPCRS and count as an annual addition for the year they were required.
but what of contributions made between 10/15 and 12/31? That's right. it makes no sense. you make them timely for purposes of satisfying the safe harbor, you actually avoided getting into EPCRS, why should the annual additions apply to the year made rather than the year required. even the IRS admits this may be issue. (On the other hand it doesn't sound like you will be running into a 415 issue either year, so it probably doesn't matter in this case.)