Storyline publish file deleted files out of computer folder of same name

No offense to anyone but I am not new to Storyline. I have been publishing in the same way since Storyline came out. I do know how it works as I have developed hundreds of courses and published for LMSs in SCORM 2004, SCORM 1.2 and AICC, along with publishing for WEB and frankly any other way to publish.

This is the first time I have seen this behaviour and it is startling! In know way should authoring software overwrite/erase its own assets.

There is a glitch somewhere and I will try to recreate it and document my exact steps so that I solution can be found. I will also change my process to avoid this happening in the future but will have to have my other developers follow suit moving forward as we cannot afford the extra time necessary to rebuild the folder structure!