First of all, welcome to the R'n'D forum, mat!

(Forgot that when I already replied to another of your posts...)
I really appreciate that you (apparently) take a fresh look at R'n'D, mentioning some of its oddities that long-time users maybe do not notice anymore!
After extracting Emerald Mine Club into the appropriate folder, when you want to change custom graphics, some entries on the graphics list are duplicated. For instance, Amiga Mine 1 appears 3 times on the list.
Yes, that's right. Especially when looking at the EMC collection with its high number of level sets (of which many have custom artwork), this really does not work well at the moment.
The reason why Amiga Mine 1 appears 3 times on the list (with exactly the same names, which is even worse), is the following: That level set comes with two different artwork sets for the game element graphics -- one that was designed for the Amiga ECS chipset (old Amiga 500 style), and another one (with more colors) that was designed for the Amiga AGA chipset (newer Amiga 1200 style). These should be named as such (like "Amiga Mine 1 (ECS)" instead of simply "Amiga Mine 1", for example). These two artwork sets are referenced from the level set's file "levelinfo.conf" for the two modes (that can be selected from the setup menu).
As many EMC level sets share the same custom graphics, these artwork sets (graphics, sounds and music, if available) are not part of the level set, but exist as separate sets (with no levels, but only artwork) that are referenced from the level sets that use this artwork (to prevent numerous diplication of always the same artwork over many level sets).
Additionally, many level sets have individual title screens -- these exist as small level set specific graphics sets which only contain definitions for these title graphics (but no additional element graphics, for example). As R'n'D currently does not now this (that this graphics set does not contain graphics that could be used by another level set in a reasonable way), it just offers these "custom graphics" (that are in fact only a few title screens) as another custom graphics set.
Therefore, "Amiga Mine 1" has the following graphics sets with the same name:
- "Amiga Mine 1" (that should be "Amiga Mine 1 (ECS)")
- "Amiga Mine 1" (that should be "Amiga Mine 1 (AGA)")
- "Amiga Mine 1" (that should be omitted, as it only contains the title screens for that set)
To improve this, R'n'D should be changed to make a reasonable decision about what artwork sets to show, and which to omit, I think. Besides omitting title-screen-only graphics sets (which would have to be detected), it could be argued that all these ECS and AGA graphics sets (and probably all the other graphics sets from the EMC collection that do not differ between ECS and AGA graphics) should not be displayed at all (as many of them do not differ much).
Instead, things could be changed in a way so that artwork sets would have to set a flag saying "this artwork set could reasonably be used as an alternative artwork set by other level sets", and let R'n'D only show these few sets (unless a setup option "show me ALL artwork sets" is selected that is "off" by default). This would reduce selectable artwork sets massively (as only manually "flagged" sets would be displayed by default), but may make sense that way.
As I am currently working on an update of the EMC collection, I will try to at least add "ECS/AGA" to the corresponding artwork sets. Not showing the title screen "artwork sets" will require a little bit more concept and programming work...