mirami:
The disappearing faces may have something to do with the scale of the model. Small size models with microfacets are a known limitation in Sketchup. The workaround is to scale up by some factor like (10), perform the operations, and then scale down by (0.1).
There is a native tool to "repair tiny triangles" in a right click menu after selecting the perimeter edges. If it does not show up, there is also top line menu Tools>Utilities>Create face. This could end up being a lot of "knitting", as I call it.
(It may be better for you to direct your questions in the other thread "on designing a shoe".)