"The SPS Museum in Srinagar is just off of the Jhelum in Srinagar, so it was very hard hit; under water for two weeks. If there were any manuscripts, they would certainly be very badly damaged in the main, and some destroyed. The distressing thing is that apparently the lack of expertise in the museum has resulted in some not so badly damaged items (including textiles and manuscripts) being dried in the sun, which would be further damaging! 

"Another negative: no one seems to have a clear inventory of the manuscripts that were there. Also, there is some ambiguity as to how many manuscripts there are in the museum. (Some say up to 248 or so, but no clear idea.) Apparently Nehru had many moved in the late 40s and early 50s. I've been following the fate of the Gilgit material because about a year ago I was able to access the wood covers to the sutra manuscripts, with the 7th - 8th century paintings on them, which seemed quite in tact. ... But since then they were moved to the museum and were apparently in the basement. So almost a sure shot for destruction. Disastrous. Trying to find out more...."

So it doesn't look good at all...