The first suggestion that will be offered by most designers is replace repeating fields with a table. There are logical reasons for using repeating fields, but the problems their use cause often offset the design ease of display.
If the repeating field is in one table, it might make sense to create an intermediate database for import, that way you have greater control of the process.
Trimming a clone of the database may be faster than constructing from a blank database.
More information about the data structure would be helpful.
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I hope after you get everything back up and running that you take two lessons to heart, one small, one huge:
All databases should be backed up frequently, with numerous sequential copies preserved and stored in at least two completely separate physical locations. Such back ups should have minimized or elminated the need for the rebuild that you are having to do.
Repeating fields aren't usually the best design option for a FileMaker database.