If you save out a .dds from a paint program that supports them you should have the option to save with no transparency - if the prog allows a choice.
You may not need to do this and thereby keep the alpha channel intact in case you need them in future and decide to swith the transparency back on.
If you want this option - try instead setting a different - non default transparency setting in the script file transparency part (insert one if necessary) for a segment or alternatively for an entity specifying a texture transperency setting in the editor propeties dialogue box.
I use a setting of 2 for transparency - if you change the setting trying either specifying 1,3 or 4 for varying object types that may force a transparent texture to render as opaque. A little test will show which setting to use for which object type.
That may work and save permenantly removing alpha channels in textures.
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