It really sucks that we all have to keep learning this lesson over and over. Everyone I've ever spoken to that has a good backup strategy in place has it because they have lost irreplaceable files.
Have real backups. Syncing is not a backup strategy, raid is not a backup strategy, etc. 3-2-1 At least three copies in 2 different (storage) formats and at least one copy offsite. It sounds like overkill but you have to decide how much your data is really worth.
It IS a pain and I don't know that there is a way to fix that. As I said though you have to decide what your data is worth to you.
I personally use http://duplicity.nongnu.org/ and a semi-complicated system of cron and bash script to backup my files to my local server, some flash drives and s3.
Getting a Time Capsule is pretty convenient if you're a Mac user. That you can add USB drives to the Time Capsule also allows you to store extra discrete snapshots using other backup software like Crashplan.
Have real backups. Syncing is not a backup strategy, raid is not a backup strategy, etc. 3-2-1 At least three copies in 2 different (storage) formats and at least one copy offsite. It sounds like overkill but you have to decide how much your data is really worth.