If you transcoded Premiere would export a lot faster. If Premiere can just dump those frames directly into a new file without changing them it can export really fast. I rarely use filters on an offline cut so exports of a 90 min movie take about 6 minutes (mainly for the audio). Over time this could add up to a lot more time saved than the initial transcode cost you.
But as you correctly identified, this could cause problems when reconnecting back to the online media. The only way I can think of doing this would be to also transcode the online media to the new frame rate. I can see why you would not want to go down this road but that footage will need to be converted to the new frame rate at some point in the process anyway.
So it really depends on whether you want to save that export time or not. If it were me, I would transcode it. It could also prevent problems where Premiere and another app like Resolve may interpolate the frames differently and produce different results.
My software:
Pro Maintenance Tools - Tools to keep Final Cut Studio, Final Cut Pro X, Avid Media Composer and Adobe Premiere Pro running smoothly and fix problems when they arise
Pro Media Tools - Edit QuickTime chapters and metadata, detect gamma shifts, edit markers, watch renders and more
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