On the Olympus site to update FW, I see V3.0, V3.2, V3.4
There is no V3.1 which my camera now has.
And there is no V3.5
It sounds like V3.1 must have had a problem and has been removed as a choice.
And it sounds like the same for V3.5
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These are the changes to be made with V3.2 and V3.4
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INCLUDED IN FIRMWARE VERSION 3.4
- Focus Stacking Mode is now compatible with the M.ZUIKO DIGITAL ED 150-400mm F4.5 TC1.25x IS PRO lens.
- Video image stabilization has been improved.
INCLUDED IN FIRMWARE VERSION 3.2
- Focus Stacking Mode is now compatible with the M.ZUIKO DIGITAL ED 12-45mm F4.0 PRO lens.
- When the EVF Auto Switch is set, you can now select how the viewfinder is displayed when the monitor is open.
Off: Disables the eye sensor. Press the

button to switch between the EVF display and the monitor display.
On1: The eye sensor operates regardless of whether the rear monitor is open or closed. Press the

button to switch between the rear-panel monitor Live View display and Super Control Panel display.
On2: The eye sensor does not operate while the rear-panel monitor is open. Press the

button to switch between the rear-panel monitor Live View display and Super Control Panel display.
When you update the firmware to Ver. 3.2, the camera's settings (except the date and time) are reset and menus will be displayed in English following the update.
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Don't know what in V3.1 they may not like.
As for V3.2 and V3.4, I do not have either lens that is mentioned for focus stacking.
V3.2 has a new option for EVF Auto Switch. Not certain that I even need this as I am happy with how it currently works.
And V3.4 improves video image stabilization. I don't do many videos, but perhaps this would be worth loading
And since V3.5 is not offered, perhaps the problem you bring up is not going to happen?
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With a little Googling I find that V3.1 added this on Jul 9, 2019 which means that I had ignored it. Doesn't say what may have caused them to remove it from update options. As far as I can tell, I am not experiencing anything impacting the performance of the camera. Here is what was once offered:
Olympus has just issued the new firmware 3.1 for EM1II:
- Stability of operation when shooting still images has been improved.
- Stability of EVF operation when the camera is turned on has been improved.
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With some additional Googling, found what was added in V3.5:
06/09/2021
Firmware update Version 3.5
Following features have been added to the current function:
Possible to use focus stacking photography with M.Zuiko Digital ED 8-25mm F4 PRO.
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This makes me think that the problem you are experience started first in V3.2 where they played around with the EVF Auto Switch ???
And it makes me hesitant to do a FW update at this time.