Time Machine not "remembering" external hard drive backup after not being connected for some time I use Time Machine on my MacBook Pro (late 2011, macOS Sierra) to back up my internal hard drive and an external hard drive containing heavy files such as video, etc. This worked great for about a month: each backup would contain separate folders for my internal drive and external drive, even if my external drive was not plugged in (as it most often is not, since that drive is mostly used for long-term storage).

However, today, when I added a file to my external hard drive and plugged in my backup drive, it began backing up the ENTIRE contents of the external drive again... which, I hadn't noticed until now, was because the backup files stopped including my external hard drive and would only show my internal hard drive. So, I'm very confused, and I'd rather not have to waste some 400 or so GB of space on my backup drive with this copying of data... Anyone know what might be going on here? It seems to me like Time Machine somehow "forgot" I had a second drive to back up... And yes, I checked the "Exclude" list in Time Machine preferences (Can Time Machine back up an external hard drive in addition to internal one?).
Once a backup interval happens where the external is skipped, you might end up with two copies. Getting partial recognition of unchanged files to have them deduplicated would require a lot of scripting to recreate hard links across several folders. 

I usually set that drive on a shelf and buy a new one. Once the new one has sufficient backup history, you could check for deleted files or just wipe the "broken" drive. The risk of not realizing a file was corrupt or deleted is slim but exactly what a backup is designed to do. 

In the end, you'll need to evaluate the cost of a new drive and the cost of potentially losing a file you could have recovered and minimize your risk and budget costs.