Save As - Not working as expected - Lost progress I thought was saved

As I've been playing I've assumed that using Save As could be used to make permanent save files even as I was overwriting auto-saves because they appeared on the Load menu as if they were primary save files until they were recycled.  After building a new colony I wanted to go back and work on a different colony but found all progress lost because I had only been overwriting auto-saves for all previous colonies.  I lost several hours of progress on multiple colonies due to this misunderstanding.

It isn't specifically stated by the save prompts that permanent saves are only made by either saving directly to the original colony save file or when creating an entirely new manually named save file.

I like the naming convention of the auto-saves.  I thought I could save time not having to re-type it for a new and permanent save file by just selecting the auto-save from the list.  I was wrong.

It would be appreciated if one or more of the following suggestions were considered:
1) When "Save As" is used to overwrite an auto-save, please write the file to the permanent save folder instead (or offer the option to do so)

or make it more clear in the overwrite confirmation that overwriting an auto-save file does not make a permanent save file (less ideal)

2) Auto-populate the "New Save" dialogue box with the current colony name and cycle number

3) Keep a number of most recent auto-saves for each main colony file rather than a global auto-save limit that deletes auto-saves of other colonies 

Thanks!
Other than losing all of my progress to the confusion I've really been enjoying the game! ^_^