You should make the quarterly payment (and future payments) online to the IRS via EFTPS or direct Pay. You can print a receipt and there is no getting lost in the mail
EFTPS is a little more complicated because you must apply and then wait for an IRS letter with a security code for verification purposes
If you stop payment on the check, and the IRS finally gets it and tries to cash it the IRS may penalize you for a dishonored payment. If the check is not cashed within 180 financial institutions are not required to honor the check but some do so to avoid a double payment you should stop payment.
however, if the IRS never gets the check, then it might impose penalties for failure to meet the prepayment requirements. this leaves you with a ugly choice. if you don't stop payment and send a second check. if the IRS gets both it will cash both.
at filing time you could include a letter explaining what happened so hopefully the IRS will not penalize you. But that would require paper filing your return since manual documents can't be attached to an e-file. the other choice is to e-file and wait for any penalty notice. then write back explaining what happened and ask for waiver of penalties