@FellippeHeitor dev 45fed46 WIN 10 x64 Pro build 21H1 (Aug update)
I may have omitted the obvious but...
When I have the dev build in the folder "A:\QB64_dev\" and my also with my stable build (v2.0) on    "C:\_QB64\"  - (note that v1.5 stable is on   "C:\QB64\") then when working with the exact same file to debug (i.e. no changing ever of filename or path) - debug does not "remember" the selected watch list WHEN I RESTART QB64.exe. 
It only seems to "remember", for me, the selected list when just re-running the program (F5).