There's a bug in the updater: it uninstalls apps even if there is not a replacement.
TO REPRODUCE THE PROBLEM:
1. Wait until there are two or more updates to be downloaded.
2. Begin the update process.
3. Cancel each of the downloads.
At the end of the downloads, the updater will uninstall all apps to be updated, then will discover the update files are not present and display an error for each of them. (Sure would be nice if the updater had a log, the error display vanished rather quickly.)
TO FIX THE PROBLEM:
The updater should NOT UNINSTALL any program until it has VERIFIED that the update file HAS BEEN DOWNLOADED and IS AVAILABLE.
BACKGROUND AND DETAILS:
My internet connection is DSL. At best it is 2.5 megabits per second, but it is often as slow as 50 kilobits per second. I may think I've got a good connection when I start something like a video or a PortableApps update, but then it becomes apparent that the throughput has become molasses in January. I typically stop the update and wait, take my laptop to work, and do the update there (gigabit ethernet, sweet!).
A couple of weeks ago, I found my Thunderbird was missing. I moved the Data folder elsewhere, installed Thunderbird again and moved the Data folder back. I thought it might have something to do with a recent canceled update, so I decided to keep an eye on the next update.
Today, I started the update and the internet connection went to practically zero. It had already started downloading something, so I hit the Cancel button, once for each app until all the downloads had been canceled. The updater proceeded to try to install everything it had been told to download. It uninstalled all the apps in the update session, and then was unable to update any of them. I looked in my Thunderbird folder (because Thunderbird had an update available) and found nothing but the Data folder, help.html, and ThunderbirdPortable.exe.
When I tried to repeat the update, there were no updates available. I checked Help > About > Apps, and none of the apps I had seen in the update list, were installed. So the uninstalls were done completely (except that the Data folder, help file, and XXXPortable.exe were left behind).
As far as my instance of PortableApps was concerned, none of the recent updates were installed on my laptop. I checked this by looking to see which apps were missing the App and Other folders.
You did get something right in all this. When I re-installed Thunderbird, I first backed up the Data folder elsewhere, but I did the install over the top of the carcass of the previous Thunderbird. Then I compared the saved copy with the original. Identical. The installer saw what looked like the remains of a prior ThunderbirdPortable and left the Data folder alone. Excellent. I'm presently reinstalling all the other apps that the updater trashed, and I don't have to worry about my settings.