@ svsanchez: let us talk about some basic's...
if i remember correct, you use a older WB-Version and not one of the latest versions 2.11.x or 2.12.x?
and we talk about different link targets to different extern URL's?
or do you mean only intern links to subpages of your project?
some thoughts about the automatically replacement of every http (doesn't matter, which method (output filter, droplet, search and replace in database)) :
not every (extern) domain works with https and it's possible, that you get a 404, if you replace the http with https without test's - on the other side: nearly every domain with https has a redirect for not-https-request's
for intern links to subpages of your own project: wb use normalize wblinks for intern links and if you change your WB_URL in the config.php to https, all the WbLinks using also https