Now your metering is normal.
You say you used to take good pictures in an Indoor office at 1/125, F5.6 and ISO100 that is certainly not right...
impossible in fact if your office isn’t a solarium or a special light testing lab...
that environment is about 7-8 ev for iso 100 that would be something more like f2.8 1/15
With the settings you used you were at least 5-6 stops underexposed.
For that aperture/speed the correct iso would likely be in the 6400 range
I looked at your camera extended manual
The (wrong) setting you used to have were automatically compensated by the auto lighting optimizer
- exposure compensation
It is the [+/-] setting at the bottom of your viewfinder. It could have been previously set at +5 resulting in severely under-exposed images, and now is reset at 0. If you want to be sure not to accidentally modify it look at page 449 of the manual for how to disable it in custom functions. Better keep it active though if you can remember to keep an eye on it and adjust it as needed.
If the exposure is too dark, turn the <6> dial clockwise while holding
down the button (for increased
It is very easy with manual settings to overlook that the small exposure bar is way, way on the far left (> -5) Even very experienced photographers sometimes dial up settings they want and forget to check it.
I think this is the likely culprit in your case, the manual refers to it in pages 136 & 160. It camouflaged the original underexposure issue.
If the image comes out dark or the contrast is low, the brightness and contrast can be corrected automatically. This function is called Auto Lighting Optimizer. The default setting is [Standard]. With JPEG images, the correction is applied when the image is captured.
In Basic Zone modes, [Standard] is set automatically
And p 160
z If [z: Auto Lighting Optimizer] (=136) is set to any setting other than [Disable], the image may still look bright even if a decreased exposure compensation for a darker image is set
Your present “predicament” is either due to the exposure being correct now, hence not needing auto ajustements and/or you accidentally switching off that auto compensation (which is a good thing) and now you are seeing the images at their native state.
N.B. You may be tempted to reset it at the wrong values to continue taking pictures the way you were but réalise that you pay a hefty quality price for that sever under exposure. Sometimes you do it if you can’t get the picture otherwise but it is generally better to increase the iso, or do both like underexposing by 1-2 stops and increasing the iso by 3-4 stops