Once a signal is added to the wave window, even if it is deleted (Delete), it continues to be stored as a log (wlf) until the simulation ends (End Simulation).
This may slow down the operation, which can be remedied by deleting the target signal from the log using the command
nolog.
Example: command to remove from the log
VSIM> nolog -r /example_sim/test_node
Example: command to restore to the log
VSIM> nolog -reset
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Category: simulation
Tools: ModelSim®-Altera® FPGA Edition
Devices: -