First to let you know that export from the OJS 2 and import to the OJS 3 is not supported, if you are trying to do that.
Second, yes, export/import does change the URLs (also articles IDs), so the DOI metadata should be manually corrected.
For the end I have a question why you are doing this? Joining two journals into one OJS (that is is the only reason I would assume)? If you want to upgrade the OJS version that should be done directly using upgrade process without import/export and it preserves the URLs.