Apache error 500 on large file uploads (mod_security)

The fact you have a ModSecurity alert means that you can't have empty activated_rules folder or you are including the rules in some other way.

There are known problems with ModSecurity for this error and it seems very susceptible to false positives.

The main advice when I rule is raising too many false positives is to just turn off that rule (I'm assuming it's rule 200003 that's firing but replace the id as appropriate):

SecRuleRemoveById 200003