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Since you asked multiple questions let me try to help you with them separately. On the .htaccess file disappearing, is it actually being removed or just not displaying in your FTP program? Some FTP clients won't display .htaccess files, even though they are still there. You can check if this is the case simply by putting a special rule in the .htaccess and then checking if the rule is still enforced after it seems to have disappeared.
On the mysql connection error, that's a bit tricky as it depends on whether the error was server level or just for the one client. From a hosting perspective, when there's a connection break for any reason you want to address it right away. However, on a shared hosting server there can be hundreds or even thousands of customer sites setup, so once you correct the problem at the server level you are somewhat depending on customers to alert you as to any individual problems which may still exist. If mysql was functioning properly at the server level but for some reason became unavailable or misconfigured for an individual customer the host needs to be told of the issue in order to correct it. If, as in your example, the customer doesn't bother looking at their own site for over a year then they haven't told the host there was a problem, so how are they to know?
You could argue that the host should have checked the client's site, but even that idea has a problem. Again, from the host's perspective, what if you visit a client's site while that client is upgrading/updating/changing their database or software? You're likely to see any number of errors or issues, but they're phantom problems that don't even exist. They just appear to because the client was working on something.
No host that I'm aware of would ever want a customer's site to be offline (and deindexed by search engines) like you described, and they'd likely be ready and willing to address this as soon as they were made aware of it, but when an issue isn't server-wide there's a reasonable expectation on the customer to bring any individual problems or issues they're having to the host's attention.
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