It is possible to run the Inoculate process (for example) during business hours. Files that are open will be skipped, flagged and reported in the reports as being in use. These files could then be inoculated in a subsequent run of the Inoculate process, at a time when the files are not in use.
However, the best practice is to run LinkFixer Advanced after hours or on weekends, when most files will be closed and accessible for processing.