Readers of my columns know I'm bullish on Qualcomm (NASDAQ:QCOM) for two key reasons. First, I think the company's wireless patent licensing and royalty revenue streams are far more defensible than some fear. Second, I have been extremely positive on Qualcomm's chip business, particularly as the depth and breadth of its mobile chip technologies seems unmatched.

However, not long ago, rumors surfaced suggesting Qualcomm's latest Snapdragon 810 applications processor was suffering from some technical issues. Qualcomm never explicitly refuted these rumors, but it assured investors that the Snapdragon 810 is on track to begin shipping in devices during the first half of 2015. It even announced a modem upgrade for the Snapdragon 810, boosting its capabilities from category 6 LTE-Advanced speeds to category 9.

Now, though, J.P. Morgan analysts reportedly claim Qualcomm is having significant issues with its implementation of the ARM (NASDAQ:ARMH) Cortex A57 processor. The analysts believe this could push out the release schedule by three months; it also reportedly will have interesting implications on the applications processor choice for the Samsung (OTC:SSNLF) Galaxy S6.

Qualcomm getting the boot from the Galaxy S6?
According to the J.P. Morgan report, Samsung is set to use its own Exynos applications processor and Exynos modem chips for ">90%" of the Galaxy S6 phones launching in February. This, the analyst notes, is in stark contrast to prior flagship Galaxy S flagships in which Qualcomm's Snapdragon chips reportedly powered ">70% of the volume."

Now, if you'll note the language in the report, the analyst said such a switch is "highly likely" and by no means a done deal. Furthermore, I do not believe Samsung's modems support CDMA, the 3G standard used by Verizon (NYSE:VZ) and Sprint (NYSE:S)

While Samsung could conceivably use an Exynos applications processor and an Exynos modem for LTE (assuming Samsung's modems are certified on the major carriers), to my knowledge, the S6 sold on carriers that use the CDMA 3G standard could require a discrete 3G chip from Qualcomm to work properly (unless Samsung has added support for this standard in its modems).

What are the implications here?
If it is true that Samsung is showing Qualcomm the door for the S6 and is broadly deploying the Exynos applications processor and modem, then this might spell bad news for Qualcomm's premium Snapdragon chip business.

While Qualcomm has other customers for its highest-end Snapdragon 800-series chips (LG, HTC, Sony, and so on), Samsung is very likely the highest-volume and most visible high-end smartphone provider next to Apple (NASDAQ:AAPL) (which uses its own applications processors). If Qualcomm is shut out of Samsung's high-end phones and tablets in the long run, then the business case for spending the significant research and development dollars on the higher-end Snapdragon processors starts to look a lot shakier.

Time to panic?
As a Qualcomm stockholder, the question on my mind is whether it's time to panic. For now, I'll play it cool and "wait and see." If the Galaxy S6 comes out and most models feature Samsung applications processors, then it will be time to ask some tough questions and perhaps reconsider the Qualcomm investment thesis. If this turns out to be just a bunch of hot air, then Qualcomm investors can breathe a sigh of relief.

I don't think it's time to panic yet, but investors should keep a close eye for any leaks while they wait for the official Galaxy S6 launch.