Is the IRS fleecing small businesses for taxes they have already paid?

A friend of mine, and several of his friends who own construction contracting companies have just received interesting letters from the IRS. The IRS claims not to have paperwork that had been filed in the past. It seems that paperwork they have filed years ago has gone missing. The IRS is now stating that they no longer have records of these companies having paid their estimated quarterly taxes for various months in 2007 and 2008. Though the companies have ready proof of prior filings, the burden of proof is none the less on them. There is an interesting footnote in the small print. It says that this letter must be disputed in writing within 30 days or the taxes that the IRS has lost records about must be paid AGAIN… even if the company can prove they paid them in the first place. The letter contains prominent telephone contact information for the IRS. During several telephone conversations with representatives never was it mentioned the need to send a written letter to dispute the IRS claim. Though the IRS agents seem to be working out the dispute cordially, the small print warning requiring a written response is glossed over. The small print warning states that federal law requires that the company be liable for the disputed funds if the written dispute is not received. How many businesses will call the IRS and begin working out the problem in good faith only to blindsided by small print and forced to repay taxes they can prove they have already paid? Has anybody else received notifications similar to this? I would think it a fairly normal paperwork mistake were not so many people I know to have received such a similar letter in the same month.