Slobodan is right, LR will keep the last five values of custom crops. As far as I know, there is no option in LR to delete unwanted ratios (e.g. you want only three instead of the possible five).
Having said that, the custom crop ratios are stored in the LR catalog (a sqlite database), so they can be edited with any sqlite editor (available free) if you feel like doing it.
Look for the value "Adobe_customCropAspects" in the table "Adobe_variablesTable"
Another option, which I don't recommend, is to create a new catalogue