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Updating Bibliographies On the Fly [duplicate]

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I am using the Classic Thesis Template. With Zotero, Standalone, and TeXstudio.

Everything on my Thesis is perfect thanks to this Awesome template. But... I cannot figure out how to correctly update my Bibliography as I am Writing. I export my Zotero.bib file then use the names in that file for my \cite{example} citations within my thesis.

Every time I update the .bib file with my new additions to from my Zotero Library, my references in the LaTeX .pdf go all Haywire? Sometimes the whole reference list disappears, sometimes half the references still work and half turn into (?). Most of the time when I try and \cite{}it cannot recognize the correct citation name from the .bib file even though I am certain that the name is correct.

Randomly it starts working again... sometimes... depending on the order that I re-run the program or delete old files or do a special dance for the gods.

I assume it has something to do with my .aux files or the .bbl file or the .tex file not getting updated correctly? I need to know the correct order to overwrite a .bib file and have it smoothly transition into correct references in my thesis. Without loosing connections to other references that have not been changed in the update/overwrite.

Cheers in Advance. :D