The next version of Calibre (version 0.7.19), due to be releasedd in the next day or so, will support editing the "I'm Reading" list on the Kobo. There are three different options for managing what Calibre refers to as Collections.
I have been using the code regularly during development and it seems to work fine. However, you will no doubt find issues that I will need to fix in the next release ;-).
Get used to the ability to manage the list using Manual Management and then start tagging books and using Automatic management as you get used to it.
Backing up your Kobo and Calibre library is probably a good idea. A better idea might be to let the brave and foolhardy go first. ;-)
1) Manual Management:
This is Calibre's default unless you have previously modified the "Preferences-Sending books to device" option for Metadata Management.
In manual mode you connect the Kobo, Calibre determines which books are on the device and displays "Im_Reading" (for books on the I'm Reading list) in the Collections field of the device view.
To edit the device collections simply double click on the book you wish to edit (in the Collections field). The only supported collection is Im_Reading. If you enter other data in the field it will disappear the next time you connect the device.
Note that you can double click and edit other fields currently but the changes will not get transfered to the kobo.
Manual mode must be used if you wish to include kobo format books on your I'm Reading list. Manual management may not be be supported long term if Calibre gets the ability to export kobo format books to the library.
2) Only on Send:
Not fully supported. In theory it works however because the book you are sending to the Kobo will not exist in the database until after you disconnect the kobo from your computer, Calibre cannot update the I'm Reading list for the new book.
Do not choose this option.
3) Automatic Management:
To use this option you need to click the "Preferences" icon and select the "Sending books to device" option for Metadata Management.
Like "Only on Send" this option uses the Tag named "Im_Reading" to manage the collections. If you want to put a book in the Kobo's I'm Reading list, it must be tagged (in the library) with a tag named "Im_Reading".
This option will remove all the books currently on the Kobo's "I'm Reading" list. Then it will add any books on the device, that have been tagged in the Library with the Im_Reading tag, to the list. That is, it replaces the Kobo's I'm Reading list with a list of books generated from books tagged with Im_Reading.
This is the recommended setting. However because the book must be tagged in Calibre's library it does not support kobo format books.
This is important
Automatic management will not be able to add kobo format books to the I'm Reading list and will remove all kobo format books from that list.
Bugs should be posted at
http://bugs.calibre-ebook.com. I will keep an eye on the Calibre and Kobo forums but you would be amazed what I can miss...
Tim