There are two options for running the linter on a design containing out-of-context (OOC) runs. To run the linter on the top design and its OOC modules, generate the output products of the OOC runs first. To run the linter on individual OOC runs, use the -srcset option:
synth_design -lint -srcset [get_property SRCSET
[get_runs my_IP_core_synth_1]]