Predict the Falling Rocks
Perl 5: 98

98 including 2 command line flags.

#!perl -p0
1while/
/,($x="($`)")=~y!#!.!,s/#(.*
$)/%$1/+s/#$x?%|%$x?#/%$1$2%/s;1while s/#$x\./.$1#/s;y!%!#!


Explanation:

#!perl -p0 #read entire input to $_ and print at the end
/\n/;($x="($`)")=~y!#!.!; #calculate pattern matching space
                          #between two characters in the same column
                          #looks like "(......)" 
1 while s/#(.*\n$)/%$1/+s/#$x?%|%$x?#/%$1$2%/s;
                          #flood fill solid rock with %
1 while s/#$x\./.$1#/s;   #drop loose rock
y!%!#!                    #change % back to #