Borrowing somewhat from @guy038 's technique of the lookahead assertion proposed as a solution for this posting: https://notepad-plus-plus.org/community/topic/13761/multiple-copy-paste-notepad , here’s a way of solving the problem presented in the current thread using only ONE Replace-All (instead of TWO as proposed earlier).
Find-what box: ^(\d{2}:\d{2}:\d{2})\.(\d{3})(?=.*?(\d{2}:\d{2}:\d{2})\.(\d{3}))
Replace-with box: \1,\2 -> \3,\4
Search mode: ☑ Regular expression -AND- ☑ . matches newline
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