I have opened multiple instances of Vivado tools and have done several actions in each. When I look at the vivado.jou file, it only shows the Tcl commands from one of the Vivado instances.
Is this expected?
When you open multiple instances of Vivado design tools, the Journal file is overwritten by the latest instance that was opened. The commands in the journal file will all be from the latest instance that was opened.
This can be avoided by having the journal file written to a non-default location.
Use the -jou switch when launching Vivado.
CD to a different directory before launching Vivado from command line.
See also: (Xilinx Answer 55459)