I already have TSA Precheck and am now applying for Global Entry. What happens to my TSA Precheck ID if I proceed with my application? Does applying for Global Entry affect my existing TSA Precheck in any way? Will I end up with two IDs? Are there any issues with adding Global Entry when I already have TSA Precheck?
TSA Pre-check and Global Entry are independent programs, administered through different federal offices (TSA and CBP, though both are under DHS). Access to Pre-check is a perquisite of Global Entry enrollment, not a component of the Global Entry program itself. In fact, there's no mention of Pre at all in its description, only as the last bullet point on the benefits page.
Already having TSA Pre-check when you apply for Global Entry doesn't hurt you, but neither does it help you. You don't get a discount on your GE application, and you don't get to skip any forms or interviews. You get to use the TSA Pre-check line while you're waiting for your GE application to be processed, and that's about it.
Once you are cleared for Global Entry, you will indeed have two Known Traveler Numbers, only one of which you can attach to any particular airline reservation to request Pre access. For simplicity's sake, I would advise you to decide which program you intend to keep and renew going forward, and to use that number exclusively. There are various rumors online that one number or the other increases your chances of getting approved for Pre-check, but none seem to be substantiated in data.
Note that the KTN is mainly about expedited screening at the airport. In terms of the main purpose of the Global Entry program, which is expedited processing for international arrivals to the US, you don't need to have it on your passenger record, nor even to have your card with you. Your passport number is what identifies you as GE-eligible.
In consideration of all this, anyone who is looking to enroll should check out NEXUS first. It's only $50 and includes both Global Entry and TSA Pre-check as benefits. The downside is that there are fewer facilities that process NEXUS applications, so it may be much less convenient.
SENTRI also includes Global Entry and TSA Pre-check access, but costs $122.25, so it's probably not worth the premium over Global Entry ($100) unless you make a lot of land crossings into the U.S. from Mexico. Global Entry is only $15 more than TSA Pre-check alone, so it's probably "worth it" for more people, especially those who make other international trips.
Global Entry provides all the benefits of TSA Precheck (referencing the comparison chart Dorothy pointed out). In particular the CBP ID that is assigned as your Global Entry membership number can be used as the Known Traveler Number for airline reservations to get TSA Pre encoded on your boarding passes in exactly the same way you use the TSA Precheck ID number now. Since Global Entry provides this plus expedited processing through US immigration (and, if you carry the card, access to NEXUS lines though security in Canadian airports, though not the NEXUS machines at Canadian immigration) I suspect that going forward you'll probably want to let the TSA Precheck membership expire and maintain Global Entry alone.
While I'm not sure how interdependent they are, note that TSA Precheck and Global Entry applications are made through separate web portals, suggesting they aren't closely integrated. All Global Entry/NEXUS/Sentri ID numbers I have seen have "98" as their first two digits so if your current TSA Precheck number does not start with "98" I would also assume the Global Entry membership will come with its own Known Traveller Number. As the TSA Precheck FAQ has a question about having more than one KTN with an answer starting with
You may use any active KTN that you have been assigned.
my guess is that your current TSA Precheck membership will continue on unaffected by the GE membership (how else could you have more than one KTN?) and that either KTN will work for airline reservations for as long as both memberships remain valid.
This obviously involves speculation, though, since I've not done this. When you find out the right answer please report back!
What happens to my TSA Precheck ID if I proceed with my application?
Nothing. You will still be PreCheck.
Does applying for Global Entry affect my existing TSA Precheck in any way?
It might change why you have PreCheck, through Global Entry vs TSA application, but it doesn't matter, you're now PreCheck and Global Entry.
Will I end up with two IDs?
You will receive a Global Entry card which is unrelated to PreCheck.
Are there any issues with adding Global Entry when I already have TSA Precheck?