If both VHF and UHF frequencies are present, it is likely that one SDR would not be able to observe both simultaneously.?
However, if the satellite has two UHF or two VHF frequencies, it is possible for both the Raspberry Pi and the Linux system to observe them simultaneously.
Has this issue been encountered before?
if the SDR can cover both frequencies at the same time (really really unlikely) then yes. For example, the RTLSDR can only do 2.56MSPS, which means that the maximum signal frequency difference is 2.56MHz (slightly less than that actually).
What are you trying to achieve ?
There aren’t many satellites that send on multiple frequencies, if those are cubesats it will have an big impact on the power budget.