Can you check a couple of settings ?
Don't have an answer for you but maybe we can explore some possibly relevant settings:
What is your current values for:
1) Options - Preferences - General - Path - Default path to save new projects ?
And for 2) File - ProjectSettings - MediaTab - Path to save media files ?
3) Lastly, if you save a project with: File - Save Project As ...
and you select your external drive location, does your project end up where you expect ?
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