I'd not worry. It's done! If a file is imported into a project like your 96K one - and it is the right pitch and the right length is HAS been re-rendered. Forget it's origin.
Audio DAWs seem to do this process automatically. In video editors, it's always a snag - they tend to bring files in at the data rate of the project - so you discover an audio track that is the wrong length and wrong pitch, which you have to fix. Audio DAWs seem to not allow mixed formats in a project, so fix them for you, or in some, warn you, or ask you. I suppose video editors just import the data, assuming all is good. Audio ones at least notice!
The downside with mixed files is that the up conversion created duplicates of the original data to complete the file that had 50% missing. You then throw half away when exporting at the lower data rate. The accuracy of the clock introduce a few errors I'd guess, where the 'created' data might be left in and the original data thrown away, changing the waveform, but I'd doubt it would even be noticed..