First set the Quotas. Set the condition for first 1000 respondents using quota  count display end of survey then anything more than 1000 display different end of survey message.

Is it ok like this ? I put the Finished label as a quota but sure it is correct.

Set embedded data at end of survey (CompletedResp =1). So whoever answer the last question this embedded data will have a value. Use this in Quotas. 

Then you can use the method I suggested above

Adding on more details…

Since quota option only occurs when quota count has been met, I think you should stick to default end of survey message if you wish for those respondents after 1000 to receive the default message. 

Then, in survey flow, add a branch logic that checks condition of quota either “less than or equals to 1000” or “has not been met” (pick one will do). Then, within that branch logic path, add a “end of survey” element and customise it into the specific message that you wish for the first 1000 respondent to see.

Thank you very much, I’ll try :)