luchopb It sounds weird that just doing a texture repack causes the textures to downscale more and more. Do you have some kind of script in your Unity project that works on all images? For example, is it possible that there is something working against all textures to reduce their weight and that this is affecting them?
If this problem is not reproduced when you create a new Unity project and try to repack the textures into it, then there must be a problem in your Unity project.

luchopb Is there a way to avoid downscaling without increasing the max size to 4k nor reducing texture quality?

I'm afraid no.

Why is it downscaling when it seems to still have a lot of space in the texture?

Unfortunately the actual texture repacking operation is just using Unity's Texture2D.PackTextures function (here in code), which unfortuantely provides just a minimal input parameter set. We would love to control downscaling during packing, but unfortunately it's out of our hands. We can't really answer why it does what it does unfortunately. Perhaps you could get some answers on the Unity forums, but I'm afraid it will likely be "you can't avoid that".