I am currently manually inputting my encrypted private keys and secret key (password) on https://www.browserling.com/tools/aes-decrypt



You should consider each and every one of those private keys as compromised and never use any of them for anything again. Likewise, consider your password compromised and don't ever use it for anything and/or change it if you've used it anywhere else!
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Is there a way I can input more than 1 encrypted private key at a time? I have hundreds of encrypted private keys I want to check for any btc balance.
So each private key is encrypted separately? It's not a single encrypted file... but a file of individually encrypted keys? 

The only way you'd be able to do them all at once, would be a script of some sort that could read the input file, and then individually decrypt each key and output them all to another file.
Can you please tell me how a script can be made. I am so lost now.
btw.. luckily none of the addresses had any btc in them. but there are like... 1000s more to go. Thank you for your concern and your advice will be heeded going forward