Trouble Google Scholar Indexed after Upgrade V. to V.

previously I used OJS.V.3.1.1 without any indexing constraints from Google Scholar, after upgrading OJS.V.3.2.2 a problem arose indexed by Google Scholar and I tried for search engines, articles could still be found (PKP, Google) but google scholar could not find.
In the settings / distribution menu, Google Verification is installed. Does it require different verification codes for each host journal?
due to a security problem in the location of the files folder, the folder I moved to root and I have a problem pdf can not be indexed by Google?
How do I solve this problem?