Today I updated Aptana to the latest public release, namely:
Aptana Studio 3, build: 18.104.22.168212131616
After restarting, all my projects forget their publish settings it seems.
The remote servers are still available in the "remote view", though the link to the project has dissappeared.
On each project, the publish submenu only shows the "Run web deployment wizard" subitem.
After running the web deployment wizard again for a project, testing and saving the settings the regular submenu items appeared again. Though after a few submenu clicks it dissappeared again, reverting back to only showing the "Run web deployment wizard" menu.