Question about best-practice way to selectively migrate passwords

Thank you so much for your help! I am very excited to get started aggregating my passwords. I do have one more question (below):

Because you need to export data first, you will have to save it in a file temporarily. You could edit this file directly, removing what you don't want to upload, and then import the remaining list in 1Password. You can now delete the exported file.

I understand. I guess one concern I have is if it is possible to take additional precautions with this plaintext file. I will try to do a malware scan on my computer, but I am concerned that a program could possibly read the file while it is getting generated. Is there any way to get the password file encrypted as it is generating (i.e. right out of the gate), because otherwise I figure I would have to open the file to encrypt it, and that this could cause even more security issues.

If there is no alternative, I guess I would just need to change the important passwords that I am removing from the file right away, to ensure that the passwords in the password file are no longer correct for these accounts.

I'd appreciate your advice on this. Thanks again.