I understand your hesitation to use a plugin that doesn’t have granular options to avoid overwriting existing content when what you’re actually doing is a merge more than a restore.
You could simply use phpMyAdmin perform a search & replace on the incorrect links via a SQL query. I’d suggest cloning what you have now (merged content with links pointing incorrectly) to a sandbox installation to test this first, or if that’s not possible then be sure to backup your full DB, just in case you have unexpected results.
If you’re not comfortably familiar with writing SQL queries, then I’m sure there are others who could help with suggestions (I always need to research writing queries very carefully first!).
Alternatively there are plugins that do just specifically that – search and replace text strings (in this case, links) – in a simpler interface than using phpMyAdmin and writing the SQL query yourself.