I do not know. I can not figure out your workflow. There are layer effects (fx) which will affect the outcome. Try applying the (fx) as this screenshot and then try whatever method previously used.
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For line drawing you can just use two layers, the line drawing and a transparent layer for the fill.
Using fuzzy select tool.
Set the mode to Add (second icon)
Set Sample Merged
With a default threshold (15) enable draw mask and that adjusts as you drag the mouse in the area.
Then fill the areas with colour. Set bucket fill to Fill whole selection.
Important Edit -> Select None before moving on to the next areas.
If you can follow it, a quick video of that: https://sendvid.com/v9g5ym2c
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For line drawing you can just use two layers, the line drawing and a transparent layer for the fill.
Using fuzzy select tool.
Set the mode to Add (second icon)
Set Sample Merged
With a default threshold (15) enable draw mask and that adjusts as you drag the mouse in the area.
Then fill the areas with colour. Set bucket fill to Fill whole selection.
Important Edit -> Select None before moving on to the next areas.
If you can follow it, a quick video of that: https://sendvid.com/v9g5ym2c