Hi… Changing the Consul key doesn’t remove existing /litefs/db rows; I verified this myself this afternoon. It sounds like you may instead be in the related situation of unknowingly having LiteFS’s internal bookkeeping writes (/var/lib/litefs) fall outside of the persistent volume completely.
(Thus, it’s that entire portion of the filesystem that’s being reset, 
—regardless of Consul settings.)
This is confusing initially—and all admit that it is—due to the presence of three different persistent stores that need to align:
| typical location | purpose | |
|---|---|---|
| LiteFS FUSE mount | /litefs/ |
web application writes and reads here |
| LiteFS internal storage | /var/lib/litefs/ |
never mess with this directly (!) |
| Consul key-value pairs | (invisible cluster) | managed by Fly.io |
What do you have yourself, for the first two settings?