The website was broken over the weekend (mostly my own fault, unfortunately) but I do have good news about that – I approached the author of the plugin in question, and they had a nice, simple solution to the problem.  The offending piece of code has been moved to a different file entirely, and should no longer disappear when the plugin updates, and does not need to be completely rewritten to function.

In short: there should be no more disappearing sidebar links, and no more pages loading the wrong content (and the next page will be up just as soon as I finish coloring it).