Time Machine not "remembering" external hard drive backup after not being connected for some time
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.