Issues while updating due to missing files URGENT

I recently tried to update EB5, It was quite behind on version 5.0.36 updating to the latest 5.0.41 When I tried it failed and i started getting strange errors about missing files... I discovered that my host had a false positive hack warning on several EB5 files... And they moved the files to a quarantine folder... I moved several of them back but not all... I moved enough to get the install to run and the install did finish... I was hoping the install would replace any additional missing and outdated files.

But now I have some issues...

I can not Publish the post or close a post on the front end, I either get an error that has no text or just "invalid server error" But I can do this on the backend

There may be more issues this is just what I am seeing right now. Could there be more files that I need to move back into place from the quarantine folder? Or is there another install I can run to fix the issue? I do not want to lose the EB5 categories and posts etc...

I also have some errors that just appeared at the bottom of the site that say:

Warning: PHP Startup: Unable to load dynamic library '/opt/php56/lib/php/extensions/no-debug-non-zts-20131226/pdo.so' - /opt/php56/lib/php/extensions/no-debug-non-zts-20131226/pdo.so: cannot open shared object file: No such file or directory in Unknown on line 0

Warning: PHP Startup: Unable to load dynamic library '/opt/php56/lib/php/extensions/no-debug-non-zts-20131226/imagick.so' - /opt/php56/lib/php/extensions/no-debug-non-zts-20131226/imagick.so: cannot open shared object file: No such file or directory in Unknown on line 0

Warning: PHP Startup: Unable to load dynamic library '/opt/php56/lib/php/extensions/no-debug-non-zts-20131226/pdo_mysql.so' - /opt/php56/lib/php/extensions/no-debug-non-zts-20131226/pdo_mysql.so: cannot open shared object file: No such file or directory in Unknown on line 0