You'll probably have to record extensively, compare samples and try to figure it out. I doubt Merlin/BirdNET would get it right every time, and if it won't, it's a field open for further research.
My list of birds I don't tick on call includes: Blue Tit (churring alarm call), Bullfinch (nasal call), Long-tailed Tit (three-note whistled call), Marsh Tit vs Willow Tit (anything other than the diagnostic call), Coal Tit, tecking warblers, Goldcrest vs Firecrest, woodpeckers (other than Black or Wryneck or singing Picus sp.), Eurasian Treecreeper vs Blackbird, Chiffchaff vs Redstart (unless tecking heard), geese, waterfowl, and many others. Over time, I will be adding some species here and removing others, but--basically--you can't clinch the ID on every sound just like you can't visually ID a bird at every angle.