I'm obviously really sorry your file has disappeared - during months of testing I have never had CVBasicIDE delete anything from a sourcecode directory.
The program works on copies and never on the original file (it has to do this because the user might have made unsaved changes to the code).
When "Build" is selected from the menu or toolbar, the IDE saves the current sourcecode as "cvbasicide.bas" in the CVBasic installation folder (i.e. the "CVBasic installation" path set in Preferences where "cvbasic.exe" and "gasm80.exe" are located). Any required INCLUDE files are then also copied from the sourcecode directory to the CVBasic installation folder. The selected script is then loaded and CVBasicIDE replaces all occurrences of "game." with "cvbasicide.". The script is then processed line by line via the creation of ".bat" files, and on successful completion the output file (e.g. "cvbasicide.rom") is copied from the CVBasic installation folder to the sourcecode folder and renamed according to the name of the original sourcefile. If "Post-Build Clean Up" is selected in Preferences then log files, bat files, previously copied INCLUDE files and any files whose names start with "cvbasicide." are removed from the CVBasic installation folder (this is the only stage in which files are deleted).
This behaviour is identical to the way CVBasicIDE v1 compiled BAS files - the code which does this has not been changed. The only difference between v1 and v2 is that external scripts are used during compilation instead of "hard-coded" instructions embedded within the IDE.