i think if anything, this might even help HTC in the short term.
Google was helping Motorola too much getting back on their feet by becoming a "Google Company", subsidising their phones and with whatever software partnership took place behind the scenes.
Not too sure if the Lenovo brand will sway people into buying the Motorola in western markets as the Google brand did. In the best of cases it might not change today's reality that the Moto X and Moto G were already competing with HTC phones.
Reading forum posts, reviews, discussions and news on the internet I've come to realise people buy Nexus or Motorolas because 1. They are cheap and 2. because they are backed up by Google. It gives people a piece of mind when it comes to durability as well as hardware and software support. Some say they buy them because they are "premium products" but not even they believe that. Lenovo might not inspire too much confidence for many in this regard.
In China and asian markets HTC already has to contend with Samsung and Lenovo anyway so I don't think it will harm them more in this respect.
I think it really boils down to what HTC does next. Their HTC One 2 has to be a success and collect as many positive reviews as the HTC One did. They are already working on speeding up their updates, communicating more to the public and refraining from launching a gazillion phone models a year that just confuse people. If they can create a name for themselves as the most premium brand of android phones, with timely updates and good customer support they might be able to survive. They just need to find their place in today's market just like Apple did years ago when PCs and Microsoft dominated everything. And I think there is a place for HTC. Neither Samsung or LG are known or chosen for their "premium phones". In Samsung's case, they just hipnotise people with all their phones' gimmicky functions and then shove them down people's throats with tiredless ad campains and physical presence everywhere.
Android needs an HTC.
The One got some really good reviews but in the end it pretty much died on the vine fairly early on. Sales barely moved from day 1 and are most likely barely on any major retailers radar at this point. HTC would have to work a major miracle to even compete in the smartphone market anymore. They just never caught on and never found a good foothold with the average everyday consumer. It's a nice enough phone, but it's too much of an offshoot brand to really play at the same level the "Big boys" are playing now. (Apple, Samsung, etc)