Can a packet be marked as a time reference from a Lua script?

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Is there a function available in Lua to do that?

Currently, no. You'd have to file an enhancement request on the Wireshark Bugzilla.

Another solution might be to add a new time field in your Lua script that follows the timestamps, but can be reset to zero on the frame(s) you want it to be reset on. After those frames, you only need to add the delta time to your own timestamp. Then add the new fields as a column and you are all set :-)