Refiling the FR 2900 can result in reserve deficiencies for some of the reserve periods in the two-year period. Deficiency penalties are covered in section
204.7 of Regulation D. If a bank's entire $200 million portfolio of MMDAs, for example, were reclassified as transaction accounts by the bank's regulator, and the reserves of the bank were therefore consistently $20 million low (that would never happen, but for purposes of illustration ...), and if the discount rate were consistent over the period at 6.25%, you could have a hefty $2.9 million reserve deficiency penalty that would never be publicized, except in SEC and similar filings for publicly-held institutions.
The FR Board can waive penalties except in cases of gross negligence or disregard. They can also assess CMPs, although I, too, have never heard of one being levied.