Well the end of the trail for me… can’t open your SU2019 model. It’s good practice if your posting a model for help to save a copy of your model back to an earlier SU version. You can get more assistance that way. Not everyone is running the 2019 version. The path is SketchUp > File > Save As . There is a drop down menu in the save window that allows you to pick the SU version, SU8, SU2015 etc.
I also observe that Trim Tool (from Eneroth Solid Tools) has problems with this.
However, the native Trim Tool (from the native Solid Tools) works perfectly fine in this case.
From previous experiences I have found that the native Solid Tools and Eneroth Solid tools behave different on various cases. None of then are perfect, in certain cases both will fail.
Thus, it is good to have both tool sets installed, often this solves the problem at hand.
According to your demonstration, when you remove the tube and create the hole, there are lines inside. Does this mean that there is a problem? When I have done this type of thing in the past, that has indicated that something it not right.
I use 3mm radius hole cutters fairly often as I remember and don’t really have any trouble with them. So in theory your 4mm radius should work.
First I tried drawing a fresh 4mm radius cutter and that cut fine. Then I inspected your cutter to see the difference and you somehow have 4 extra planar edges on the cylinder. I reckon this could possibly be making the geometry too small to produce the solid output I got with mine. I don’t know how you ended up with that edge.
To test, turn on hidden geometry and erase the 4 edges that don’t connect to a vertex. Then try the solid tool again…
There’s also a slight issue with the vertices of the cutters being “off axis”. That’s nothing to do with the issue of solids but its always better to draw circles “on axis” for numerous reasons. To fix that for this one you could just rotate the cutters so the vertices lie “on axis” before using Solid Tools.
For a tiny hole like that there’s absolutely no need for 96 sides. SketchUp wouldn’t actually draw a small circle like that with 96 sides. It would give you that message and revert to the default 24-sided circle.