I don't think anyone here can give you a definitive answer to your question because people have all had different experiences when it comes to HTC's warranty department. Some get denied for tampering and voiding the warranty while another customer with almost an almost identical issue breezes through without even un-rooting.....
It is very likely they have some other means of telling whether the stock firmware/software has been replaced at some point that we have no clue about. If they wanted to be hardarses about this kind of thing I'm sure they are quite capable of doing so but I do not think it is in their best interest as a company to get that kind of PR when you have Google and Motorola offering warranties (guaranteed or something like that I read somewhere?) despite tampering. 'Power users' like most of the members on XDA, are a huge market who often have multiple devices and a high level of influence with friends, relatives, coworkers etc when it comes time for their upgrades...You can see where that train of thought ends up I hope.^^
Anyway, sorry for the ranting, haha. My point is that you should take every precaution you can including going back to S-On, "Locking" the bootloader again, and ensuring your device is as exactly like it was when you first got it if you want to minimize your chances of getting denied your warranty. You can always look back on it and go, well maybe I didn't have to go through all that trouble but sure glad it got fixed! That's a much better alternative than the regret you'd have if something as simple as S-Off is to fix(or faux fix) resulted in your claim getting denied.^^
Best of luck, whatever you decide!
Current Device: Sprint HTC One M8 Harman Kardon edition(Black with Champagne) *S-OFF* (Victim of Sunshine)
Backups: Sprint HTC One M7(m7wls) *S - OFF*(Rumrunner), Sprint HTC EVO 4G - *S-OFF* (Facepalm)
Bricked Paperweights: Motorola Photon Q 4G LTE *RIP QWERTY KEYBOARD, I MISS YOU*
Prior Devices: Samsung Galaxy S3, Samsung Galaxy S4,Google Nexus