There are 4 different rocks in Relic Path that give 1 shard each. Are you sure you have not gotten mixed up?? As far as I have found, Items only regenerate in the Hidden Grottos.
This source, Bulbapedia/ Recurring Items, mentions nothing about Relic Passage, staing only the Hidden Grottos.
These are things that can be found in the Hidden Grottos. After you have taken something from the Grotto, there is a 5% that you will find an Item or a Pokemon again every 256 steps.
All these items can be found in any Grotto.
Bold are hidden within the Grottos, so use the Dowsing Machine.
These stones can only be found in specific Grottos.
They follow the same rules of regenartions.
Routes 2, 3 (dark grass), 5, 6 (near Breeder), 7, 9, Floccesy Ranch
- Fire Stone
- Water Stone
- Leaf Stone
Route 6 (Mistralton Cave)
- Moon Stone
- Sun Stone
- Shiny Stone
- Dusk Stone
Route 3 (pond)
Source: Bulbapedia/ Hidden Grottos