I found that to be inconvenient as well - not in case of separate approach charts for e.g. RWY 09/27, but for airports having terminal vfr charts, circuit charts and so on.

For example, when flying in Egelsbach, EDFE, it is favorable (for me), to have the (bigger) terminal/arrival chart depicted at all (or most) times, as it shows me the VRPs, the routes from the VRPs to the airfield and so forth. Now, SD automatically switched to the smaller VFR approach plate, just depicting the patterns - which is not the chart i wanted to look at that moment.

Though the automatic mode is very useful in most cases, if you are flying in and out of a field having multiple charts, it can be bothersome.

I am looking forward, to have some kind of option to make the overlay (sticky - maybe a pin/tag/lock symbol!?)

Great, looking forward to it. 
The issue is very easy to reproduce:
- Create a new route direct from EHRD to EHMZ
- Select about half way the overlay for VISUAL APPROACH CHART RWY 09
- About 6NM before the airfield the plate is replaced by VISUAL APPROACH CHART RWY 27
What I also notice is that it removes my selected chart during the flight a couple of times, looks like when I'm overlaying the chart in an early stage of flight and when I'm exiting a FIS area (or something), the destination chart is removed for some reason.
What is the logic about that? That is also something I do not want during flight. I have the uncomfortable feeling that charts are removed, placed and replaced by SkyDemon during my flight, unwanted obviously.

No, that is the work we did this morning in response to the issue you raised in this thread. It will take effect in the forthcoming 3.1.1 version.

Is that already introduced in the current version for iPad? Because it is still replacing my charts when I try in the simulation mode.

What we've done for the moment is when we find two visual approach chart candidates for automatic loading, we load neither, leaving it up to the user to make an explicit choice. I think that's a good solution to the problem.

Although I have not encountered this problem in flight I certainly wouldn't want to - it could be a real safety issue. Please could you explain your solution from an operator's point of view as I don't quite understand what you are proposing.

We would certainly consider it. Has anyone else found themselves inconvenienced by this issue? We don't like introducing options unnecessarily so there may be a cleverer way to solve the problem, which is that there can be multiple visual approach charts and one shouldn't necessarily be selected automatically.

A dangerous situation occurred when I pre selected the visual approach chart RW09 for EHMZ. About 6 NM from the airfield, just before turning downwind, I noticed that SkyDemon had replaced my selected approach chart RW09 for approach chart RW27! The same situation occurred when approaching and selecting the correct plate (overlay mode) for EHGG, when navigating into the circuit SkyDemon replaced the chart with another approach plate. I was very confused at that moment, not sure what happened and questioned my selections. 
After doing some investigation, I found out that SkyDemon is auto selecting plates for you based on location (georeferencing auto selections). I reproduced the situation on my iPad afterwards using the simulation mode. A friend of mine had a similar situation where SkyDemon replaced the selected approach chart for EHHV with an incorrect approach plate now displaying the wrong approach procedure. This auto loading of plates is clearly not working when multiple runway specific plates are available for an aerodrome. Now I cannot thrust the approach charts I select anymore. Unfortunately you cannot switch this off. This leads to confusion and dangerous situations during flight. Tim Dawson, could you make sure this feature can be switched off in a next release?