Hi
>>So can I be sure that all other interrupts are not using this Data Flash?
If you wrote the other interrupts code you will know whether they are accessing data flash or not. Very probably not and a naked interrupt won't be doing so.
>>Also since I am performing the write operation in one the FTM timer interrupts itself, will it cause some problem?
Flash operations take some time (eg. 200us for word write or several 10s of ms of sector erase) but the operation itself doesn't care whether called from an interrupt or not. The impact on blocking lower priority interrupts during slow operations is the thing to consider.
Regards
Mark