Thanks tpearl5. Yes, install dir was already removed.
I also suspect there is a backdoor somewhere, or a file that is vulnerable to sql injection. I'm wondering if there are some strings I can search my apache raw access logs for to identify the culprit.
I thoroughly checked all files identified in Maintenance > Diagnostics > Suspect file versions. I found and removed a number of files that were left over from previous versions of VB and old/uninstalled mods. All the files left (current mods I am using) seem to be ok, I didn't see anything unusual in them. I replaced all VB core files with freshly downloaded copies.
VB 4.2.1 PL1 is not known to have security vulnerabilities as far as I am aware. I'll probably upgrade to 4.2.2 anyway, but I'm not sure it will fix this.
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