Solution
Yes, FlexLogger continues writing to a TDMS file if a system or module is disconnected after a log has started. When the acquisition finishes, the data file will resemble the following image.

Here, the green line represents a system that remained connected during the entirety of the log. The red line represents a system that was disconnected from NI Measurement and Automation Explorer (NI MAX) during the log. Once a system disconnects from FlexLogger, no data will be written to the file, as shown from 8:18 on the time axis.