@debra_mansperge , your best course of action is to get Canvas Support involved in unraveling this. The Canvas Guide on cross-listing sections (or two courses that represent sections) (How do I cross-list a section in a course?) is clear on this point:
Cross-listing should be done while courses are unpublished. Coursework is retained with the course, not with the section enrollments, so if a published course is cross-listed, all cross-listed enrollments will lose any associated assignment submissions and grades.
The Canvas Gradebook can currently support a total of 2000 grade changes (per How do I use grading history in the Gradebook?), a number that is relatively easy to reach in a course with 48 students (50 graded assignments/quizzes will do it). Without knowing the number of assignments your courses have, it's hard to say if the error message you're getting is because your newly-merged gradebooks now exceed that number, or if the error is being thrown simply because active courses have been cross-listed and grade history has been lost. Again, Canvas Support can help you sort this out.
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