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huh? it's a thankless job.
but i wouldn't tell you to do something knowing it would screw up your site.
clearing templates_c is practically the same as selecting yes to "Update module template .html files from themes/your theme/templates directory?" as selecting yes for that will do the same thing except it'll be XOOPS doing it instead of you doing it manually.
i suggest reading the FAQ section on themes & templates.
clearing templates_c is a viable option and will cause no problems whatsoever, unless there's a problem in the 1st place, as templates will/should be recompiled.
if you clear templates_c and then your site doesn't work, then you obviously have a problem elsewhere and is nothing to do with what i said to do..
the problem is most likely with your edited theme.html or something else.