I spent a few hours today trying to figure out the provenance of these things and wound up going pretty far down the rabbit hole. To summarize, nobody is sure. The theory that IMA went with is that the locks were English and the barrels were Indian, and there is evidence that supports (but certainly does not conclusively prove) this. Another theory is that the barrels are English and the locks are Indian, and again there's some evidence to support this as well. Most of the folks that are really into this field seem to believe that wherever the locks were made, most of them weren't made in Nepal, as they simply couldn't make something like that in sufficient numbers at that time. As if this wasn't confusing enough, Nepal was historically famous for recycling parts from DX'd guns into new ones, locally fabricating parts to get incomplete foreign guns operational, and generally doing what had to be done to make things work. Thus, it's perfectly within the realm of believability that a few of those Nepal Bess locks were indeed from EIC...but almost certainly not all of them, or even the majority of them. According to some of the guys that have spent time digging through the piles of old guns at IMA, most of the locks appear too good to be from Nepal, but a bit crude for England - hence the India theory. Of course, the competing theory goes that those locks were from England as that would have been the least expensive way to get them at the time, but the locks that were sent were not the best, possibly including locks that had failed inspection and been rejected. No one really knows for sure.
Why would Nepal take EIC-marked parts, grind the original markings off them, and apply their own? I can think of a few. They certainly didn't know at the time that EIC markings would make the parts more collectible a century and a half later, so there wasn't a compelling reason for them not to do this. If the theory about second quality English locks being sold illegally to Nepal via India is true, it may not even have been the Nepalese that ground the English markings off.
What did I get out of all of this? Unless I were there picking out my parts personally, I'd pass. A well made lock doesn't always look all that different from a basket case while it's mounted in the stock. If I knew for a fact that the lock was made in Nepal, I'd certainly pass; I've already had to fight with one of those things and I don't want to do it again. That having been said, plenty of people out there have restored them, so I may still just be overly cautious after my experience with my Traditions Springfield. Based on a couple of build threads that I read, these IMA kits often require a bit of tinkering to get running and I'm presently all tinkered out.
If you were going to go ahead with a project like this, it might be worth holding off on a replacement barrel until you know for sure that the original isn't going to cut it. It may turn out that the one that they send you is perfectly sound.