The word is made of two kanji: 復 (fuku) 元 (gen)
- 復 (fuku) means "restore"
- 元 (gen) means "origin"
Put together, the word 復元 has the following definitions:
JMDict (Japanese-English dictionary)
restoration (to original state); reconstruction
三省堂 スーパー大辞林 (Japanese dictionary)
Returning something to an original condition or place. [Restoring houses of ruins]
By brief Google survey, the main usages of 復元 seem to be for restoring data (in computers), restoring various historical items and artifacts, and so on. Not very different from the English equivalent.
By some Google searching, 復元の流れ (fukugen no nagare - "the flow of restoration") seems to be an inscription on a stone monument at the Tenryū-ji (天龍寺) temple in Kyoto, which is placed near a small man-made stream of water. The inscription "復元" appears in other locations in this temple too. They appear to be memorials for when the temple was set on fire during the Kinmon incident, or perhaps one of the many other times the temple was set on fire. I guess it's just a short phrase to remind people of the ongoing recovery from those disasters.
As far as Google serves me, I don't see any particular other usage of this phrase, other than people occasionally using it to mean like... "the (work)flow of restoration", in eg. a step-by-step guide on how to restore computer data.