Just to perhaps close the books on this, since Dolalin uncovered beta and early launch patch notes it's given a bunch of insight into evolution of game mechanics. They've been added to the wiki with links to the source material.
This is a patch note from January 1999 beta that strongly indicates flee stuns were in since launch:
https://wiki.project1999.com/Patch_Notes
Quote:
January 5, 1999
Increased chance of being stunned when chased.
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