Hello, @alexandretar,
Welcome to the Netfabb forum!
Meshes don't really have a definition for being solid. At best, they have one for being closed. Everything else is more or less inferred and assumed. Even its volume is mere convention, whether it has one to begin with, and if it does, whether it is positive or negative. Meshes are formed by continuous 2D surfaces curved or creased in 3D, and those surfaces themselves are assembled from discrete triangles connected to each other along their edges. (Whether that connection is implicit or explicit depends on the format of the mesh file.) And together, those surfaces may or may not fully enclose a volume that can be calculated ("is watertight").
Netfabb treats meshes accordingly. When it cuts, it cuts through the continuous surfaces and returns the sections. It does not assume solid material. This is by design.
Likewise, its repair (its closing of holes, specifically) generates patches of new triangles along the open edges, and the algorithm generally tries to close the hole with as few new triangles as possible, somewhat similar to how a sheet of soap water follows a wire loop. So, if you have an open edge that is very irregular in 3D, the resulting patch is unlikely to represent what you did during the original cuts. Additionally, Netfabb does not maintain any history of previous actions, let alone shapes, for triangle generation or regeneration. To the algorithm, the sections cut from the original mesh are themselves just as new and original as the mesh you loaded in the first place.
Knowing this, you can coerce Netfabb into generating better patches. By adding "pilot triangles" in key places where the open edge changes direction in 3D. With pilot triangles I mean triangles which you add manually to split holes with complicated shapes into more holes that themselves have less complicated shapes, making the patch generation more predictable. Remember, Netfabb must regenerate information, and to do so it must work off the only information it has. This regeneration cannot be perfect, but you can help with making it come close enough by providing better information.
To add triangles manually in repair, use the Add triangle command from the Repair menu.
Step-by-step use in the online help: https://help.autodesk.com/view/NETF/2023/ENU/?guid=GUID-9A42A7A5-B26F-4C06-A982-8AAB9028A6D8
Examples of closing holes after adding pilot triangles, including a brief step-by-step video :
https://forums.autodesk.com/t5/netfabb-forum/splitting-large-stl-and-shelling-for-printing/td-p/7563...
https://forums.autodesk.com/t5/netfabb-forum/error-with-export-from-skp-to-stl/td-p/8228469
Also, your mesh appears to have been generated inside-out. Meaning, its triangle data was written in the file in such a way by Blender that the side of the triangle that Netfabb normally takes as "the inside" is pointing away from the volume that the surface had originally enclosed. This might not matter to your further steps, or might in fact be required, and Netfabb can handle this just fine. As written initially, it is just a matter of convention. However, it may lead to unexpected results while you're working on the mesh within Netfabb. If nothing else, visual inspection may be hampered as Netfabb indicates "the inside" of a triangle in a rather dark red by default. (You can change this color in the settings, should you wish to do so.)
As a visual aid, try toggling the triangle edges from the View menu.
Best regards,
Steffen