Used lsregister, now keep getting app first time opening warnings

Question

I used the command
/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -r -domain local -domain system -domain user
to try to solve a problem I was having (right-clicking on a file, the "open with" menus were often displaying multiple entries for the same app). This command seems to have solved that problem but now I have a new issue as a result:
After restarting my mac, trying to open a file with an app I've used many time before (the app is the pdf reader Skim), I get a message from the OS that I am opening the app for the first time and whether I wish to proceed. For some reason, each time I restart  my mac, it forgets I have previously used this app. (This behavior also occurs with a few other apps, but not all apps are effected.)
Have I screwed things up by using the lsregister command? Is there a way to fix this?

Answer 1

Back up all data.
If you have more than one user account, you must be logged in as an administrator to carry out these instructions.
Select the text on the line below by dragging across it. Don't include the blank space at the end of the line. Only the text should be highlighted.
sudo xattr -d -r com.apple.quarantine
Copy the selected text to the Clipboard (command-C).
Launch the Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window (command-V), then press the space bar.
Now switch to the Finder and and select the item(s) that are causing the problem. Drag the items into the Terminal window. More text will be added to what you entered.
Click in the Terminal window to activate it, then press return.
You'll be prompted for your login password, which won't be displayed when you type it. You may get a one-time warning not to screw up. You don't need to post the warning. If you don’t have a login password, you’ll need to set one before you can run the command. If you see a message that your username "is not in the sudoers file," then you're not logged in as an administrator.
The command will take a noticeable amount of time to run. Wait for a new line ending in a dollar sign (“$”) to appear. You can then quit Terminal.