It doesn't sound as if you are doing anything wrong. It may be that some corruption has got into the metadata file though.
If you had a Mac I'd suggest trying to use one of the alternative merging softwares created by users on this forum, but I'm not sure if they have Windows versions.
Certainly Merged files can grow to some extraordinary file sizes and I've had 50Mb files created with very small starting documents.
Make a copy of the document and the metadata.db file and move the copies into another directory on your PC and try the merge software on those.
Howard
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