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I am running a headless full node. The first time I synced, I followed the http://iota.partners guide by downloading their current database and performing a rescan_db on first sync. Now their guide says the rescan isn't necessary. Everytime I restart and resync my node, the latestMilestoneIndex equals 243000 during the sync. As expected, the other Milestone values are 99999999999... during the sync, and I thought latestMilestoneIndex was supposed to be 999999999 also, but instead mine says 243000 during the sync, every restart. Is this an issue? Was this from the rescan of iota partners DB? I tried doing another rescan after having been synced for a few days, but it still shows 243000 during the syncs. Any explanations?

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243000 was the milestone of the latest snapshot. Therefore, if your node has not loaded or seen any transactions, latest milestone will show as 243000. The milestone hash of the snapshot will show as 999999⋯9 as the snapshot milestone does not correspond to a transaction, and the trytes conversion of all zeroes is all nines.

(This value will change if there is another snapshot)

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Apparently this is common behavior https://github.com/nuriel77/iri-playbook/wiki/IOTA-Full-Node-Tutorial---Linux#why-do-i-see-the-latest-milestone-as-243000

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