Actually, HARP is more compatible with RM2, at least in how skills are handled.
In RMSS/FRP you have skill categories, which you purchase ranks in, and then individual skills in those categories that you also purchase ranks in, and then the skill bonus is the combination of the category and skill bonus added together. Cost for each rank is determined by the cost of the category.
In RM2, you have a lot of individual skills, each of which have 2 stats that apply to it (which are averaged rather than added). These skills are divded into categories, but these categories are just a method of classification. Costs are determined for each individual skill.
In HARP, you have individual skills, divided into categories, which is used for classification (and cost is based upon category - all skills in the cat cost the same), but you do not buy ranks in the category.
So, in effect, HARP contains elements of both versions, but in its own mixture.
As for converting, if it is for NPCs, or creatures, why bother? The skill bonuses are all percentile in nature, so they are compatible straight out. Using a slightly different method of to determine the skill bonuses is not going to make much of a difference. Personally, I think that RM2, RMSS/FRP, and HARP characters could all be run side-by-side with little hassle.
Just compare the total bonus of one character of a given level with those of another from the other system. figure out the rough difference between the two and just apply a generalized bonus to all skills in the system with the lower bonuses on average.
The only thing you would really have to convert would be armor/DB. Since HARP works differently than RM in this respect, a conversion would be needed, but it is still simple. If using the HARP combat system, just look at the armor, figure the equivalent in HARP and apply the proper bonus to DB. Going the other direction, subtract the armor bonus from DB, and determine the equivalent DB.
I once played a character using an alternate skill system presented in RMCVI alongside normal RM2 characters. It was a little weaker in some spots and a little stronger in others, but on the whole it averaged out. It worked just fine and dandy, with no hassles.