A ransomware attack happened to my server, I've backups and all and I tracked down the reason to two elements (either unupdated Bitnami LAMP stack or unupdated Flask server) but I noticed some files aren't encrypted, any checks I should do to verify that I can use this files safely?
The way ransomware encrypts files is based on extensions. They add a broad range of extensions to cover the majority of crucial files for working/business/school and so on. That list is not dynamic or cloud/service based, it is usually hard coded into malware itself. At least that's what happened up until now. So if for example, ransomware didn't add .mp3 to the encryption list, it would be skipped, the files would not be affected. You can do a full scan with anti-malware and anti-virus software just to be sure, but I think the data will not be affected and you can use them safely.
Fun fact: This is why having 2 ransomware (One after another) on your computer will not do additional damage. Usually, ransomware doesn't contain other encryptions extensions.
The ransomware doesn't encrypt all the files. If you have the name of the ransomware, you can find which files will be encrypted on Internet.
To be sure that your files which aren't encrypted are not altered at all, you can write a script to calculate the hash sum of each files and compare it with you backup (if the files haven't been modify since you backup).