If you have an EIN, then at some point the IRS did know you exist, because they're the ones that issued it. They don't know that you should file, because you might have dissolved, or you might not be over the $5k threshold.
Our PTO had an EIN that the IRS didn't actually have a record of having issued; this was on our bank account. The IRS did, however, have a record of issuing a new EIN to our group, which never made it to the bank.
When I finally got through the 501c3 process and filed the 3 years of 990EZs, we got a notice that we owed some $11k in late fees. However, perhaps in some part due to the fact that we got "legal" on our own initiative, we were able to get the fine waived.
In our case, we were able to get our tax-exempt status retroactively to the date of incorporation, some 20 years earlier. Maybe your past officers were just prescient!