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That's because you are running out of memory. We don't support or recommend processing more than 100 entries at a time.

That said, you should NEVER mark all files are safe. It doesn't even have any effect whatsoever to files with a zero threat score (~95% of your site's files). Remember, per the documentation, you only need to mark as safe the files which have a non-zero threat score and which you know are safe (read the documentation for more information on how to do that). These are about 400-500 on each site, the first time you scan a site. So you only need to process 4-5 pages once and then about 1-2 pages (one page = 100 entries) every week or so depending on how many extensions you have and how often you update them.