I have an indoor lime plant that flourished through its first winter. Then, scale invaded, and I have been busy taking it to the shower and carefully cleaning leaf by leaf and stem by stem. The most recent "scale purge" found only a few affected leaves and stems that i carefully cleaned, first with alcohol, then with water from the shower and finally with a Boneem Spray. However, between the last "scale purge" about 3-4 weeks ago and the most recent, these white patches have appeared on some of the leaves. It's not mold. It looks like the depigmentation of skin in humans called vitiligo.
I think the damage may be caused by the actual sucking parts of the scale insects. They adhere tight to the plant and literally suck the sap out of it so the discolouration could well be where they were attached, like a little scar. It sounds like you’ve done all the right things to help your lime plant fight off the scale invasion but their life cycle is incredibly invasive as they start off very tiny, tucked away in the leaf nodes and bark cracks before they emerge into their full shell like size so keep vigilant as I’ve found that the minute you relax, the single one that escaped has multiplied and turned into yet another infestation! If you want to try another method of removal which is quite gentle, I’ve had some success with simple dish washing liquid, well dissolved in water,(too strong will burn the plant) and then wiped over the leaves. The scales will pull in their legs and lift off easily. The same method can be used with neem soap, lathered up between your hands and applied in the same way. Neem is particularly effective because it is naturally oily and leaves a residue which the scale insects find hard to grip onto. Be careful if applying it when the plant is flowering though as it can cause the flowers to drop. I’ve sadly lost orchid flowers this way.(Scale insect adore orchids it seems and I think a hothouse orchid from the garden centre was the original perpetrator of my problems!) Good luck