The only solution that I can see is essentially to write your own autoincrement code. Something like this:
To insert any single record:
LOCK tables
start a counter $i at 950
select record with id = $i
If record exists, increment counter and repeat
else insert record with id = $i
UNLOCK tables
This is slow, inefficient code. It will be fine if you are only using this import tool a few hundred times a day. If you are using it a few hundred thousands of times a day... or hundreds of times a minute, then you are going to need to consider a more robust solution like:
a. fix those high numbered records and reset your autoincrement number back to 1001
or possibly:
b. run an experiment where you don't fix the high numbered records and JUST reset your autoincrement number back to 1001. This might be sufficient, I'm not sure.