Q: after installing OS X 10.11.6 lost all Logic Pro plugin

it may have moved them.

do you have a TimeMachine backup, if so you can restore from there.

see this document

Latest OS X & Logic Pro Compatibility Information

What happens if you do the following files and restart?

1. Quit Logic Pro X if it is running.
2. In the Finder, choose "Go to Folder" from the Go menu.
3. Type ~/Library/Preferences in the field and click Go.
4. Remove the "com.apple.logic10.plist" file from the Preferences folder. Note that if you've programmed any custom key commands, this will reset them to the defaults. You might want to export your custom key commands before performing this step. Learn how to Browse, import, and save key commands.
5. If you upgraded from an earlier version of Logic Pro, also remove the "com.apple.logic.pro" file.
6. Restart the computer.

And also, what is in your Plugin Manager window?

Logic Pro X menu at top left

Preferences->Plugin Manager...