When it comes to web hosts alerting their customers that their websites have malware or otherwise have been hacked, what we have seen is that those many of those customers are overly suspicious of those claims. While they are issues with false positives and with web hosts having shady partnerships with security companies, in most instances the claim is correct.
There are good ways to double check the claim. Those included doing a comparison of files that the web host claims are impacted on the website to a clean copy of the same files that haven’t been on the website (say from fresh download of the software used on the website) or getting in touch with a company like us that will always determine that the website is hacked before taking on a cleanup, so you are not paying money for something you don’t need.
There are bad ways to try to double check that as well. One of those is by running the files from the website through computer based antivirus software. The reason for that is that type of software is designed to detect malicious code on a computer, not the type that would be in a website’s files, so wouldn’t even be attempting spot the type malware that might be in those files.
Using software designed to detect malware on a website also might not produce great results as from what we have seen the quality of that is not always great and that software may use the same detection that is used by the web host, so the same false positive could be produced with it as well.
Web based scanners are also not a good way to handle double checking since they usually can’t check the same things that a web host could have checked and the quality of them seems extremely poor.