Khaled,
Thanks for responding. The relationship ID is required when creating a line chart from a related table in the popup in ArcGIS Online. When the ID changed (from 7 to 4, for example...there are 8 different 1:M relationships in this dataset), the popup was not able to access the correct table to create the line chart, and therefore, it did not show up in the popup. When I investigated why this was, I realized that it had to do with relationship ID. I was able to easily fix it, but I had to redo it manually. Which, the whole point of the line from a related table in the first place was to avoid this. The relationship ID is also used in popups that reference fields from related tables, so this issue is beyond my case.
I am publishing the FileGDB from ArcGIS Pro by overwriting the feature service after each quarterly update. From your comment, it seems that the issue may lie in how ArcGIS Pro organizes the relationship IDs when creating the SD file. I would expect that the relationship IDs are created in order either alphanumerically or by Object Class ID in the FileGDB. But in my case, neither is true. It actually seems random.
If it is random, I speculate may indicate that their creation could be from an unordered data structure in the source code (such as a Python dictionary...but I know that ArcGIS Pro source is not coded in Python). Therefore, this could be a simple fix in the source code. I create the geodatabase from a Python script, so the names of the relationships classes and the order in which they are created is consistent each iteration.
Let me know if this helps. Thanks.
James