Again: even if you see (including literally with eyes) whatever particles of the modern science via some tech. means, even in the most elementary particle, rupadhammas there still can be experienced , which may be then grouped in various kalapas (lit. “groups”) ((again, kalapas are not something different from rupadhammas listed in Dhammasangani, but just particular ways to group them according to frequency in this or that specific piece of materiality)) It is not about atomism. If one were try to think of rupadhammas as of something beyond the bare giveness-of-experience, it will be only papañca, since (paramattha) dhammas are just most basic elements of experience regardless any “logic” systems upon it, be it “realism-materialism” where one is believed to be able to analyse fully separate “external world” (the field of scientific believes), or be it “idealism”, where everything is believed to be only of mind, meaning that there is nothing beyond it and that the mind itself creates all, or whatever else. Theravada is interested only in the phenomena as they appear (I’ll repeat: regardless any attempts to “explain” those via some ultra logic system with “proved postulates”), since they are the problem itself, because any elements of experience bear the marks of anicca, anatta and dukkha, and it’s precisely enough for the task to be done (attaining Cessation). And again notice: that being said, it doesn’t mean that we reject or accept any extremes, and it is not a form of idealism, since we don’t make any “logic deduction” of kind like “everything is just mind (experience) and there is nothing beyond”, we just abstain from such “need”, and work within the safe epistemologic zone in the middle, i.e. just descripting what appears as it appears in the way, which can bring about vipassana-ñanas and further destructions of the defilements, i.e it is yoniso manasikara, and the main point of the simsapa sutta.
Anyways, strictly speaking, you cannot really decisevely “prove” something beyond the phenomenological epistemology, it was pretty clear even to the western philosophy (starting from Pyrrho and ending with Derrida, via Hume in the middle), thinking is just endlessly hindered by itself (for more: see the principles of Pyrrhonism, for example).
What are you trying to do is not completable within the theravada’s epistemology, and one can “lose faith” only in the case of making wrong connections between the two doctfines, but I’ll again say: the one doctrine doesn’t reject another, they are just based on completely different foundations and complete different tasks, having different goals. It is like comparing the sky and a tea thermos only because they are blue in colour, or something like that. I would again recommend to read books on definition of paramattha dhammas, at least, for example, the first chapters of “Manual Of Insight” by Mahasi Sayadaw.