ashesinchains There are a number of things that can cause lots to become inaccessible. As you noted, residential rentals are one of the leading causes but there are other causes. Some CC and mods will do it, usually broken. Fixing it is difficult at best and more often than not, not possible. And if you have an orange triangle with an exclamation point in it over the lot in map view, that is a sign that the lot (and the save) has corrupted. If that is the case, then you should abandon the save and start a new one. It can't be fixed.
If you don't have the triangle and can't get into the lot in build mode from the map, the only thing you can really do is to try to place another lot on top of it from the map. I would suggest that you find a vacate lot of the same size and save that to your Library, then use that to attempt to replace the problem lot. You can try that several times, but chances are, it won't work and then it's probably best to abandon the save and start a new one.
Probably not what you wanted to hear but when you have the situation you do, it's usually best to start over.
Hope this helps