Did you check to see if it your population went down by that amount elsewhere in your empire? Perhaps it is a cool feature whereby the rebellion draws in population from nearby planets. Maybe.
Or maybe not. Do you have a savegame?
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SE4 Code:
L Gd! $ Fr- C- Sd T!+ Sf-- Tcp-- A% M>M+ MpD Pw RV Fq+ Nd- Rp+ G-
/SE4 Code
http://www.sandman43.fsnet.co.uk/se4main.htm