This is a question I get a lot from clients with highly modified SMF sites. The answer is simple:
If your forum was a plain installation then the update will probably find no errors.
Since your forum has many modifications the update code does not recognize the modified code and shoots an error message because it does not know how to proceed.
For instance, to have Adsense on your site you would have to modify x code on y page so it changes y page. When the update looks for x code on y page then it does not fix x anymore but a modified x.
Ignoring errors and installing anyway could bring your forum down as well.
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