Actually, when projects are merged with duplicate camera parameters box ticked, it generates and seems to support multiple calibration targets, one for each project, but actually, when this happens, the band will not align. If there are 3 projects, this will act like 12 different cameras. Also, the reflectance maps will not be merged; you will get 12 maps. Hence this procedure would not be of your interest because you will get no extra benefit compared with processing projects individually.
So you will have to uncheck duplicate parameters. With merged multispectral images, we support only one calibration target. If from one flight to the other the sky coverage, time of the day (sun position), light conditions would change then it would be hard to find the image of the calibration target that would be representative for both of them. That being said relying on a picture of a calibration target from another flight in other conditions would compound errors and is not advisable. It is not implemented in the software. As your flights were taken at such a long time between them I would recommend not using the radiometric target anymore. But if for some reasons you want to keep it then I suggest processing the flights individually and stitch the results in a third party software.
However, if these conditions do not change then you have a representative set of images of the radiometric target then you can process them together.
For more details please see the paper: https://support.pix4d.com/hc/en-us/articles/204894705
If you have 3 flights, then I would suggest you use the targets of the second flight (if all the flights were one after another).