Why the Harpers etc don't immediately go check out the Well though is a mystery....
I mean if your hunting for a cult focused on dragons, and especially one with a penchant for making draco-liches, a place that's A) called the Well of Dragons, B) a known location, & C) known to be a draconic graveyard.... You'd think someone would swing by & take a look sooner rather than later once the problems start.
First of all, the Well of Dragons isn't exactly the kind of place you go "check out." It's remote and poses obvious dangers even in the best of times. Secondly, although the Cult of the Dragon is known, the stuff it's doing (large scale raids) is totally outside of it's normal capacity or even motivations. Thirdly, the Harpers is neither a large organization, nor an omniscient one, so being able to immediately connect rumors of regional raids to the Well of Dragons right off the bat is kind of a stretch (Leosin correctly guessed that Greenest would be the next target due to studying previous targets and determining that all the smaller and easier ones had already been raided, but even that was ultimately a shot in the dark for him).
There's also some other things to consider. The treasure from raids was known to be sent far to the north via disguised trade caravans, even though the Well of Dragons was much closer and to the east of the raiding targets. The whole point of that plot was to specifically avoid drawing attention to the correct purpose and destination of the treasure by essentially laundering the stuff through the caravans, a portal, and a flying castle through the mountains. That's the adventure-specific details that the characters deal with, but it stands to reason that the cult was also obfuscating their operations in other ways, like via hired mercenaries and double agents and planted rumors, etc..
What they cult didn't plan on was some pesky adventurers (with the help of a skilled Harper agent to piece the initial pieces together) to not only track the real destination but possibly prevent the treasure from even reaching it.
It's also worth noting that -- as of the beginning of the campaign -- had someone actually decided to go physically check out the Well of Dragons, nothing would have seemed out of the ordinary. There'd still probably be a few dragons or dracoliches flying around, and the fortress would certainly be active, but that's it. It's not until the second book when the horn starts compelling dragons to show up that the cult really begins consolidating it's forces in the area in preparation for Tiamat's Glorious Return.