It is now possible to integrate Rstudio and Zotero seamlessly via the combination of the citr R package and the Better Bib(La)TeX for Zotero/Juris-M extension for Zotero. This means that there is no long a need to create a separate bibtex library for each project; instead, one can create and maintain one giant Zotero library (with many different subfolders maybe) for all projects. According to this post, it will soon be possible to work with Zotero group libraries (i.e., libraries other than the main "My Library").
01/08/2018 Correction: the group library functionality is already available in the github version of the citr package. Good work.
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