Answer:

Yes, it does matter what units are used.

If an AutoPIPE Vessel model (.emvd file) was created using SI unit, then the cost estimation should also be performed using SI units,

Under cost estimation module, go to:

File>Preference>Estimate configuration file, click on Browse and select the file "Param" which contains the configuration data in SI units.

If an AutoPIPE Vessel model (.emvd file) was created using US unit, the cost estimation should also be performed using US units,

Under cost estimation module, go to:

File>Preference>Estimate configuration file, click on Browse and select the file "Param_US" which contains the configuration data in US units.

NOTE: In cases where one want to customize, please note that it is advisable to copy, paste, rename these files, add customization, and save the file instead of configuring the original.