If you are using Pantone Bridge, or a similar service that gives you current spot-color-to-CMYK conversion values, those values are embedded in the .kpfx files being used in your tFlow scripts, and will need to be updated in those files by editing the .kpfx files in pdfToolbox.
This screenshot from the pdfToolbox desktop application shows all the spot colors setup in the currently-loaded script. Each spot color on that list in the screenshot is set to be converted to specific CMYK values, so each entry on the list needs to be updated to the current conversion values in the scripts that you are using in tFlow.
If you are a user of Adobe Switch, an Adobe Switch Exchange file could be imported into pdfToolbox to update those values and avoid having to edit those entries manually for updates.
We don't sell or support pdfToolbox directly, but it is possible that the script updates could be done through our Professional Services department. Please open a ticket at support.aleyant.com if you would like to get a quote from our Professional Services department on doing these changes for you, but keep in mind that manually editing and adjusting the list of colors does take some time.