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I was having a time-out problem with one of my infected sites. It had over 200 infected files.
… employ the fix-as-you-go method which means you click on the Automatic Fix button as soon as there is anything to fix but you let it keep scanning at the same time.
I tried that and it worked for a while.
Then a big batch of bad files came up and the Automatic Fix wasn’t able to handle it.
I restarted the scan and let it complete.
Then unchecked all the red-coloured bad files.
Then checked 10 of them at a time and ran the fixer on those. This worked.
A couple of times I tried a larger batch. At about 16 at a time the fixer started to time-out (i.e. it just kept churning away but never completing).
Currently my ADSL internet seems to be running slow. And using the modem’s WiFi (when I take the computer into the house) is even slower.
Perhaps when (hopefully) ADSL performance improves there won’t be all these time-out issues.
Even so, I think it might be helpful to have a way of unchecking all the infected files and to have a way of checking these files in batches. Maybe.