It's probably sensing the RPM of the fan on one or more fan headers. This requires 3-wire fans. If you unplug a fan, the system thinks that the fan has stopped spinning and gives you the error.
If you have at least one 3-wire fan in your system, you could probably wire in a jumper that connects only the 3rd wire over to another header and fakes it out. Essentially, split the RPM wire and send it to two fan headers.
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