Mikhail,
The issue of the JTAG controller being upset, and causing difficulties is covered in many scientific papers, like those from Los Alamos Labs (Search for Heather Quinn), also those from JPL (Gary Swift), and also NASA.
There are well known, and well characterized SEFI (single event functional interrupt) conditions that lead to the JTAG, or the configuration state machines, or the power on reset sections of the FPGA to "go crazy."
Up until V4, these rare SEFI events (which only occur in space, from heavy ion strikes), required the device to be reprogrammed, and in some cases, powered down.
Recently, the V4 QPRO product line was announced (for radiation tolerant space flight), and the testing has shown that no power down SEFI events occur, but some SEFI events may still require "pulling PROG low" to completely restart the device. Given the rare nature of these events, the devices are finding their way into many spacecraft packages, as techniques exist for mitigation and recovery that are acceptable to these missions.
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(and so on...)
Xilinx has two space effects consortia, one in the US, and one in the EU, whose members are those companies designing spacecraft electronics, and associated universities, and national laboratories. The proceedings and reports from these consortia are listed on our website, as well as appearing on their own websites.
There are recommended techniques for monitoring the JTAG, and the configuration, so that one can recover from SEFI events contained in various applications notes (which also concern themselves with "scrubbing" so single event upsets don't accumulate and "break" a TMR'd design).
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Austin