Solution
The option to select a channel as a Cold Junction Compensation (CJC) source was added to FlexLogger 2023 Q2, to be able to select this it is recommended to upgrade to that or a newer FlexLogger version.
For modules without a built in CJC, such as the PXI-6289, you need to use an accessory with a temperature reference, like the SCB-68/SCB-68A, and configure it to enable the temperature sensor in the AI0 channel, as explained in this article:
Using Cold Junction Compensation (CJC) on the SCB-68 or SCB-68A. You can then configure the temperature enabled channel AI0 in FlexLogger with a
Constant CJC source, that will provide the CJC for the rest of the channels:

For the rest of the thermocouple channels you can set the
CJC source to
Sensor and map the
CJC sensor setting to that channel created to provide the CJC:

Once configured it will look like this, taking as an example a PXI-6289 with AI1 referencing AI0 as its CJC source:

For older versions of FlexLogger, you would need to work around this by using
calculated channels to:
- Convert the CJC channel to temperature.
- Subtract the CJC temperature from a thermocouple channel.