Changes to files always seem to cause problems. I've found that the best way to reduce problems is ALWAYS check in prior to regenerating. Of course, deleting glbtbl.*, ddtext.*, dddict.* can always help.
Another little caveat that can cause problems is if you develop in DV and have generated your file in other environments (PY or PD), you need to make sure your jde.ini 'Default Pathcode=' points to your DV environment. When you generate your file, it will look for specs in this pathcode and if you had already created it in PY, for example, and this setting points to PY, it will be generating with the old specs.
Once you are absolutely sure your file is generated correctly (has all your changes. Use SQL to make sure), then change your business view and generate that.
I rarely delete fields and dont remember the last time I have done that, so that may be an issue here. Good luck.