Ok, thanks for the additional information and clarifications.
The "safest" way going forward, would be to first backup (or clone) this drive to another drive of equal or greater capacity.
However, that may not be desirable, or by not having a second drive handy, practical.
The next step would be to use the Disk Utility's First Aid option. This shouldn't delete anything on the drive. It will test the drive's integrity and, if required, make any repairs with your permission. Regardless, there is always a potential for data loss (and why, if your data is critical to you, that you should employ more than a single destination for backups.)
I suggest that you review the following article, before proceeding. Let me know if you have any questions.