Affiliate redirects hacked and directed elsewhere. Can't find/fix problem.

I'm fairly certain this isn't the best place for it but I really couldn't find a better one here.

I have my affiliate links set up in the following format
mysite.aaa/visit/productpage.xxxx
mysite.ddd/go/productpage.xxxx
with html redirects on the pointed to pages.
Well it seems someone has hijacked all these folders and every link now points to the same page. Presumably the hijackers affiliate partner as it is in the same niche as mine as a competing product/service.
But when I look at the coding which is, after all, very simple I don't seen anything tapered with or any explanation of why this is occurring.After finding this problem and looking back over my clicks/conversions it appears this has been going on since roughly the beginning of June. Ouch. I had been wondering why my earnings had plunged.
What can I do short of wiping out all those folders/files and starting from scratch?
Where is this code hiding?

Thanks for any help on this!

Well, I've fixed most of the links on my site by creating a new folder, /go2/ and populating it with all new redirects for each product/service.
The new ones work just fine but unfortunately, changing out every link on my site is quite the job so only the most visited pages/posts have been fixed.
No ideas on what's going on here?
What about prevention going forward? That is even more important but my security knowledge is, at best, lacking.

Are you using a CMS for hosting?