The short answer to the linker problem was that almost all global variables were defined in the defs5.h file. That file is called by several of the source files. In the case that the source files are compiled separately, space for the variables will be assigned multiple times. Apparently, IDE8_3 was able to compile the project in one go which means that the defs5 file was read only once.
In our case we defined a macro for EXTERN which changed the EXTERN to extern unless a separate #define was set (in main() only) . This worked for the majority of cases and brought our linker error count down to ~100. The rest were handled individually.
The long answer is more complicated. We had a recurrence of the problem of importing projects and their source code into a new workspace. This was the topic of two previous posts. When we have more time, we will revisit those posts. Briefly, we had a problem with starting a "new" project. The new-project wizard would not accept our input for the chip and board files in step 5. The browse buttons brought up totally empty screens.
We even re-installed the IDE (no change).
We now mark this post as "solved"
jDrum