The Version Number is used to trigger a reread when content has changed.
The version is entered manually and should be incremented starting from 1, however any digit can be entered. Compliance Tracker 365 only checks for a difference in number to trigger a reread.
For pages, make the changes to content in draft, including the increment of the Version Number, then Publish the page when ready.
For documents, overwrite the file - DO NOT DELETE THE FILE. If the files have different names, update SharePoint or the new file to have the same name before uploading. When ready, increment the Version Number and if needed, publish and approve the document.
If you have deleted the file in error, see if it can be restores from the Recycle bin. If not available, historic reads of the original file will not be visible in reports.