Can your Sophia credits be rejected when applying for a Master?

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There are a few factors in play here. One is getting admitted. A grad school will look at the total package of your application, what degree(s) you have, what school you graduated from, your grades, your professional experience, references, essay, etc... When it comes to your grades, they will typically compute a GPA based on your transcript. Some school look at all your courses, some at the last 30 or 60 credits, etc... Since alt credit is typically not graded they can't use them to compute their GPA. Typically, the better the rest of your package, the less important your GPA will be.

Another factor is prerequisites. In addition to degree requirements, programs will often have prerequisite courses they want you have taken at the undergrad level. Some schools may decline to accept alt credit to fulfill those prerequisites. Typically, they will allow you to take those courses at their school (which can be expensive) to start the program. If you know what those courses are, then you can arrange to take them from an RA school rather than as alt credit.

If you have a particular program in mind, you should contact them and discuss these concerns NOW, before you plan your degree. Grad school admissions offices are typically much more responsive and helpful than undergrad ones, so don't hesitate to reach out.

If you are willing to be flexible about your grad program, then we have found that it's perfectly possible to find programs that will work with your DIY degree, and plenty of people have done so successfully.

I don't have a specific school + program that I have to go to.

I will likely have a list of 10 to 20 schools that I'll apply to.