The IRS says that using certified mail will serve as proof of timely filing. However, if you file electronically, you get an electronic receipt from the government and you do not have worry about your return getting lost.
If you do mail your tax return, what's the worst that can happen? If the IRS owes you a refund, you'll figure out after a few weeks that there's a problem. A call to the IRS will determine that your return was never filed. (If it's past June 1 when you re-file and get your refund, the IRS has to pay you interest on what it owes you.) When the IRS owes you, there is no penalty for filing late.
If you owe the government money, as much as a year might go by before the IRS sends you a letter asking why you didn't file. At that point, you provide your copy of the return and a copy of your check register showing the check you wrote for the amount due (properly dated and in the right order, of course). I think that would suffice to get them to waive any penalties for late filing. You'd have to pay interest back to April 15, but you would have had the use of your money all that time because your check was lost in the mail.
