Maybe it's not dead. I don't have an Aquaero but recall they have PWM port overload protection. The manual for the Aquero 5 & 6 says the following about port protection. I don't know if the 6 LT is different in this regard but probably not.

aquaero 6:
Maximum current is 2.5 A per output independent of output voltage, resulting in
a maximum power of 30 W at 12 V. Outputs will be switched off if amplifier
temperatures reach a critical level and will automatically be reactivated when
cooled down. If an output current of 3 A is exceeded, the output will be perma-nently
disabled. To reactivate the output, the aquaero (or the complete PC) has
to be disconnected from power for a short period of time. The fan outputs are
short-circuit proof.

You didn't mention what was plugged into the problem port. Was it a fan? if yes, PWM or DC, and what model? Was it a pump, or a splitter? What speed was the port set to? If the port drive transistor got too hot, it would have recovered automatically when it cooled down. Since yours is (I assume) staying dead, it's not that. Could the output current have exceeded 3A? Try doing a full power cycle of the Aquaero or the whole computer. Disconnect whatever was plugged into that port first. Attach a single, known good fan. Maybe the port will reset. If it does, the Aquaero should be OK but you will need to check whatever was plugged into that port - fan, fan extension cable, etc.

No they don't specify how long power has to be removed to reset a port but I'm pretty sure that 30-min is long enough. I think your port may be dead. The EK-D5 Vario pump has a 4-pin Molex connector for power, Are you using that to power the pump? If not, read on. If you are powering the pump from the Molex, then I don't know why the Aquaero port died.

If you are powering the pump from the Aquaero, it may have overloaded the port. Here is a LINK to a recent thread about powering an Aquacomputer D5 Vario pump from an Octo PWM port. In this case, the OP thought that this would be OK to do, and it did work for a while (like yours). OP was advised by Aquacomputer that it is NOT OK to power a D5 pump from an Octo PWM port because of the high in-rush current when the pump starts up. According to Sebastian (Aquacomputer dev), the absolute max current draw for an Octo PWM port is 2.1A, and a D5 pump can draw over 4 amps of in-rush current. The Aquaero 5 & 6 manual says the ports on the Aquaero 6 have a maximum current rating of 2.5A. The EK-D5 probably exceeds that during in-rush.

There is also this interesting note in the product description for the Aquacomputer D5 Vario pump (see below).

Important: The Aqua Computer D5 pump has an optimized PWM input and can be used with any Intel PWM standard compatible fan controller. This pump can be used with aquaero 5/6 PWM fan outputs without any heat dissipiation at the aquaero. All other currently available (as of January 2015) D5 pumps with PWM input use different hardware that will not work correctly with the PWM outputs of aquaero 5/6 devices. This pump is compatible with nearly any PWM fan controller on the market.

I am not sure exactly what this means, or what is different about the Aquacomputer D5 Vario pump. I could not find an Owner's Manual for the Vario version but the product description says it has a 4-pin Molex connector for power and I assume a standard PWM fan connector for control, just like the EK-D5 Vario. In this note it is not clear to me if they mean you can power an Aquacomputer D5 pump directly from an Aquaero PWM port but not other D5 pumps. In the thread I referenced above, OP was told he cannot power an Aquqcomputer D5 Vario from an Octo port (2.1A max) because the pump can draw over 4A during in-rush. I think this means it would also overload an Aquaero PWM port, but the note seems to indicate that the Aquacomputer D5 is different than other D5 pumps, so I am confused. Hopefully, an Aquacomputer rep or someone more experienced than me will chime in here. Despite whatever the difference is in the Aquacomputer D5 pump, they seem to be saying you cannot power a "regular" D5 pump from an Aquaero PWM port. If you were, and were not using the Molex power connector, this probably blew up the port.

No problem - happy to help. Sorry you could not get the PWM port working on the Aquaero. It's strange that it worked for such a long time before it died, but that is also what happened to the OP of the other thread I referenced. I was hoping an Aquacomputer rep would chime in here and explain the meaning of the note that I quoted in bold for the Aquacomputer D5 Vario pump. Sometimes their documentation can be a bit vague. Enjoy your D5 Next!