Yes. It is possible (and advisable) to run inoculate again right before moving your files to the new location.
If you will maintain (not “clear”) the database between the initial and "incremental" runs, LinkFixer Advanced will check the time stamp of the files against the data in the database, and will skip the files that have not changed. In the case of files that have been changed, only new or changed links will be inoculated.
Even if you do clear the database, and LinkFixer Advanced scans and re-inoculates the entire data set, LinkFixer Advanced will ignore any links and child files that were previously inoculated. So, there is no particular danger in running the Inoculate process more than once.