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cmhsieh54,
It is a known issue that the Companion Software will hit some internal limit when merging documents with lots of scribbles. Where this limit is exactly, is unknown. Some of reported this after 20 pages of scribbling, you hit it only after 45 or 50 pages.
The only known workarounds are using the third party merging software available here on MR or the laborious task of deleting all scribbles that did merge correctly and then merge again and repeat until all scribbles have been merged.
Groen
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