I don't completely understand this question.

You can write a Tcl procedure (e.g. invoked from a macro toolbar button) that use the commands you want (GiD_Process to send keywords to be processed by GiD to do thinks, like do a cut, and Tcl commands/procs , like GiD_Graph, etc.)

Probably is not a good idea to mix the information of the nodes's coordinates and the data of the conditions. If you are designing this input format and are free to modify it you can re-consider it. In any case, if the input format cannot be changed: GiD provide the special command GiD_WriteCalculat...

you can write a small batch file with the GiD process commands to be done e.g. my_file.bch MEscape Files Read "your_path/your_model.gid" MEscape Meshing Generate Yes DefaultSize MEscape Utilities Calculate escape escape escape and then invoke GiD with -b to process this file gid.exe -b my_...

Try resetting the GiD user preferences
http://www.gidhome.com/documents/faqgid/Solve%20problems/Reset%20all%20user%20preferences

The main problem of this model is the bad shape of some surfaces (like the surface 3246 of the 3volm_beforemesh.gid), there are self-intersections of intersections with neighbor surfaces that prevent the creation of the volume mesh. I attach some pictures of the problematic shape, and some mesh of t...

Sorry, this question must be asked to SAFIR developers, we doesn't know the features of this code

No, the old numeration is not tracked or stored.
If do you somehow define results on the mesh, these results must use the current id of nodes and elements.

You must try to avoid write a mesh files+results using these 'huge jumps' in numeration of nodes or elements.

The problem is the content of your file, not the graphic card. You have attached a 'GiD postprocess mesh ASCII file' that is using too big integer ids for the nodes and elements. MESH "Soil" dimension 3 ElemType Hexahedra Nnode 8 Coordinates #node_number coord_x coord_y coord_z 1001001 0 0...

Attach a zip with your GiD model to do some meshing tests.

It happen only with this model or with all models? Probably is a problem related with the graphic card and some OpenGL feature. (if only happen with this model, attach it) By the image you are using OpenGL by software (safe visualization mode) In general, if possible, is better to use the hardware a...