You need to cure each Damage application.
First we'll start with the effects stack. The effects of multiple spells of the same name do not accumulate. However, as you have pointed out, this does not matter.
The effects of different spells add up while the durations of those spells overlap. However, the effects of the same spell cast several times do not combine. In contrast, the most potent effect, such as the highest bonus, of those releases applies while their durations overlap, or the most recent effect is applied if the pieces are equally powerful and their durations overlap.
Then, Harm's most powerful application will be active. Any minor damage reduction application from HP will be inactive, but present. There is nothing in the rules that suggests that the effects of spells are superscript, but they are eclipsed. So, if you reduce a creature's hit points by 30 with one throw and 20 with another in the next round, the creature's hit points will be reduced by 30 for one hour. One hour later, your hit points will be reduced by 20 in 1 round, since the second throw would still be present in the target.
How diseases are cured, what number is cured and what diseases are cured are beyond the scope of this question, but once one of them is cured, the other still remains.
Why not all at once?
The end of Harm reads as follows:
Any effect that eliminates an illness allows the maximum point of hit of a creature to return to normal before that time passes.
There are two ways to read this. The first is a global application of this rule and the second is a contextual application. In the first, one could argue that everyone The reducing effects of health would be eliminated along with the disease. This is the wrong way to read it. To suggest that a single cured disease eliminates all Damage applications, a global application of this rule would be needed. And that simply is not feasible. This spell would be out of reach. It would mean that you could eliminate the effects of reducing a vampire's health by eliminating the disease if the target also suffered damage.
Therefore, the second form requires that we treat this final clause as affecting only each individual Damage release. In the same way that each spell gets its own damage roll and saving throw, each effect must be considered as its own individual "sickness". So a cure for an application of harm.