We need isogen output files to be overwritten/replaced. This option is checked in the project manager, but when we isogenout the files take the line number and adds alphabetic sequence.

Checked the .opl text file switch 31 - it's set to "11"

When it is time to run the isos for the final time, we empty the iso folder so the numbering starts back over.
I dont think I have seen isogen overwrite files.

I have found that the isometric files are overwritten when Isogen is run the first time in a new CADWorx session.

+1 You can also empty the input folder where the PCF's are stored.

My isogen overwrite existing output files without deleting files in input/iso folder.
Funny thing is that it is working ok on my home computer but it is not working on my company computer. Of course I test in same setting.
Only different thing is.. I am using 64bit CAD & CADWORX 2010 at home but 32bit CAD & CADWORX 2010 in the company.
Also I found that whenever I run ISOGEN in 64bit CADWORX, it generate .XML fle as well as isometric drawing. (For example, 5555.i01.dwg, 5555.i02.dwg, 5555.i01.xml)
But 32bit ISOGEN did not generate .xml file.

Does "overwrite existing output files" function working on only 64bit Autocad & CADWorx?
IF so.. is it because of the .xml file?

Does anyone know how to make .xml file(5555.i01.xml) with isometric drawing files(5555.i01.dwg, 5555.i02.dwg) in 32bit AUTOCAD & CADWORX ?

Please tell me if my guess is wrong.

It's working now

The solution is very simple..
Install the latest build of CADWorx.
==> http://icas.intergraph.com/forms/ICAS-Product-Downloads

AND..

change a setting in I-Configure :
- OverwritePlotFile = TRUE

Good luck!