The Resource assignments to the Tasks cannot be "merged" when importing seperate SP files into one master file, when working withthe same schedule.

It is not recommended to work in separate SP files if working with the exact same schedule it. Although, if you are working on separate schedules in separate SP files, those can be successfully combined in a Master SP file.

A workaround could be to transfer the assignments so to speak from one file to the other.
1. Create a Resource User Field "Tasks" with the following settings:

2. In Navigator>User Fields, press "Recalculate Values"

You can see that the Task IDs for assignments have been added as a UF value

3. In the other SP file, File>Import>Synchro Project skipping all except the following. If the file has Appearance Profiles, 3D Paths, and/or Resource Codes that are not in the other file, Import those as well

4. From Assign Resources ribbon, select Auto Matching>Resources to Tasks and create a New Rule

5. After saving the Rule, press Search, then Assign All

Do note that you will have to go in manually and change the Resource Appearance Profiles for any assignments that do not use the standard Install profile, and  also have to reassign 3D Paths to Resource assignments.