Pixhawk logs not clearing

My Setup:
Quad, Pixhawk Clone (v2.4.6), MP v1.3.74 bld 1.3.756327684, Copter legacy v4.0.5., APC props and plastic frame, Taranis X9D+ TX, Taranis X8R RX (SBUS from RX to Pixhawk clone).

It seems that every time I complete a flight test, download logs, and then clear logs, the logs do not actually clear. Even though I give it 30+ seconds, and MP says the logs are cleared i.e. no logs to down load. When I down load the next time I see older logs that I had cleared. Anyone have an idea of why this may be happening?

It could be related to this:

The temporary answer is to leave all the logs on the SD card, starting with 00000001, or eject the SD card and manually perform operations directly in a computer.
The fix is in 4.1 DEV so hopefully we get that soon.

Thanks xfacta Shawn, I will watch for the update to fix this.