Feature Request - Synchronise Option (in addition to Equalise)

I have a similar if not the same issue and the only way, or I should say the easiest way to get around it is to do as you suggested and use mirror (very carefully). I'm wondering if using folder exclusion (i.e. on "Archive") would prevent half the problem at least. The other half of restoring no longer needed files, I don't have a solution for. Honestly, I don't think there is an easy solution to the entire problem, but it is a perfectly reasonable issue none-the-less. I'd be interested to hear what you have in mind.

I love Toucan, but not for something like that.

For that level of complexity you might try something like SVN instead. It's a tool typically used by programmers, but I find it useful for file sync. With SVN, a repository is stored on your computer. It keeps track of all changes made to every file, including deleting, moving or renaming files (but you have to do these through SVN for it to see the change). You do not work with the repository itself. Instead, you create a "working copy", make changes to that as you normally would, then using the SVN client "commit" those changes to the repository. The SVN client compares the working copy to the repository, and records all of the changes.

Why is this convenient? If you want to work from an external hard drive, just put a working copy on there. Make all the changes you want. When you get back to your computer, commit the changes to the repository. Then update the working copy on your computer and it will get all of the changes, without silly things like duplicated files. Later, when you've made changes on your desktop, update the working copy on the external drive. Here's were Toucan comes in; backup the repository periodically so you don't lose your stuff when your computer breaks.

There are some down sides. You'd have to learn how it all works, which isn't difficult, but much of the documentation I've seen stinks. Working with binary files can be slow. SVN also keeps a history of all changes to files, which is really nice if you decide you liked an older version more (or if you delete something on accident), but can take up a bit of space. Even still, I've used it for a 450MB project with mostly text files, but some binaries, and I'm happy with it. Tortoise SVN is a nice SVN client for Windows (with decent help documents).