Your published verion (as per File > Publish Settings) should go to a sub-folder called /web, under the project folder structure. Unless you explicitly change the 'Target' folder that is where it will go.
One thing you may have done, and I suspect is the case, just go File > Save As and notice a new option to the bottom, left of the Save button, called 'Save in Folder'. This allows for multiple compositions to be saved separately instead of 'jumbling' all the items into a single location.
See Edge Animate Help | New features summary for reference regarding this feature.
Darrell