Ubuntu 16.0.4 - Update linux-generic

We have recently been patching our Ubuntu servers and have found that the following three updates linux-generic, linux-headers-generic and linux-image-generic cause Influx data to corrupt and we have to refer to a backup.

When we looked at the Inlfux data it did appear to be there but it appeared that the Shards had corrupted.

Has anyone else seen this issue and any suggestions on how to install these updates without causing data corruption would be greatly appreciated.

Thanks in advance.