I just found a "Helium-hole" from atmospheric data provided here. I was actually looking for this, and the first search was immediately succesful, a hole was found from;
Time: $05.01.2002$, $05:00$ UTC
Place: 68 Latitude, 0 Longitude on $112-138$ km height,
It's is shown in the picture below. As the picture shows the derivate, thus below 1 the amount is decreasing. The absolute amount was $-25.7\%$ less at $122$ km height than the peak above at 139 km. The absolute amounts were $3.294 \times 10^{-7}~g~cm^{-3}$ at $122$ km height and, $4.434 \times 10^{-7}~g~cm^{-3}$ at $139$ km height.

As Helium is chemically unreactive under all normal conditions. And the temperature was $245~K ... 629~K$, and pressure $6.7 \times 10^{-4}~Pa...4.7 \times 10^{-3}~Pa$, which I consider "normal", as this vacuum is merely a "medium vacuum".

Thus there must be some physical reason for this, which I am just not aware of?

This question is related; Why In Thermosphere is He and O divided as measured?

Helium hole

Edit; It seems that the this is not actaully a hole. The picture below shows how the amount of Helium is actually constantly higher above $140~km$ height.

Helium in Atmosphere 5.1.2009



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