Temporary solution:
using the "glove" icon should dive you underwater if you possess the flippers (no need to equip).
Also, using the glove icon in proximity of a railroad track would do the same thing as having used the draisin (if you possess it), no need to equip. (Not as viable of a solution***)
This would still allow the sword to be the same, and for you to carry a bow, bomb, or morph while taking advantage of the new diving features.
***the draisin esuggestion could be implausible sans some directional (parallel)and onwall checks.