Try exporting as a idml file.
Could also be scripted very easily
If Trevor's suggestion doesn't work and your file is just messed up (and you have to fix it), here are my thoughts.
If you used paragraph styles for your numbered lists, and you didn't use local overrides (for example, to restart the numbering here or there), you should check the paragraph style to see if it is set to continue from previous number or begin at 1. If the latter, change to the former. If you need to restart numbering (and you're not using styles already), there are two things you can do with styles that work.
One is to make a duplicate of your number style set to begin at 1 and apply it only to the first entry of a new series that you want to start over, and use the original numbered style for the rest of the list.
Another thing you can do works best when you want the numbers to always restart at 1 if you're dropping numbered lists within sections of body text. You set the body text as a numbered list starting at zero, and remove the code from the Number section (^#.^t is the default code) and any special indent you had specifically for the number. The body text will look the same, but any numbered text after it will restart at 1 (actually, it will continue to 1 from the 0 that isn't showing in the body text). If you want some lists to continue after body text, you'll need a duplicate of either the body style without the numbering parameters, or the number list that always starts at 1 like in my first example.