MacOS – Applications in Dock not showing ‘open application’ indicators

How to Rebuild Launchpad Database in OS X Yosemite (10.10) and Later

1. Go to Library folder, which is hidden. To access it, click anywhere on desktop and make sure you see word 'Finder' in the top menu near Apple logo.
2. Press and hold alt/option key and in the top menu bar select Go and finally Library.
3. In the Library folder, locate and open the Application Support folder.
4. In the Application Support folder, locate and open the Dock folder.
5. You'll find a number of files in the Dock folder, including one named desktoppicture.db, and one or more files starting with a dashed set of capital letters and numbers and ending in .db. An example file name is FE0131A-54E1-2A8E-B0A0A77CFCA4.db. Grab all the files in the Dock folder with the dashed set of letters and numbers that end in .db and drag them to the trash or press ⌘/command + delete keys.
6. Launch Terminal, located in the /Applications/Utilities folder.

7. In the Terminal window, enter the following:

   defaults write com.apple.dock ResetLaunchPad -bool true; killall Dock

Launchpad has now been reset. The next time you open Launchpad, the app will rebuild the databases it needs. Launchpad may take a bit longer than usual to launch the first time, and the Launchpad display will now be in its default organization, with Apple apps shown first, and third-party apps next.

It will be very difficult to isolate the issue to individual preference files, since there could be several subtle issues.

Better to take the opposite approach - start with no preferences and only copy the old preferences over one by one as you come across them. That is, as you discover that you have a preference that needs updating, find the single preference file that will give you that preference, and restore it. Re-test and only proceed if things are still stable. Will be a drawn out process, but necessarily so I think. When you can no longer add individual preferences, consider the restoration finished and many set the remaining preferences.

This complex relationship between the OS, Applications and user files is why Apple created Migration Assistant. It might not be help here but it is useful to know just how intricate the process is of "migrating" from one OS version to another.