please invent non-sensitiv data for your use case.

Can you make up some random but representative data?

For example, it sounds a lot like you're parsing a URL for GET parameters, so your data with fake customer data with might be:
http://www.example.com/random_funky_characters_here.html?name=JoeSmith&address=123UniversalAve&CreditCardNumber=1234567890&kneecapstate=broken

my $inrec='0;1;2?foo=duh;3;4;5;6;7;8;9;;;;;;';

You've already given some input data, presumably faked to the necessary degree. All you needed to do was to give a couple more fake input record instances and their corresponding output records to make the needed transformation(s) much more clear. No "customer sensitive" data need apply.

I thank everyone for their replies so far. I have updated the input examples. INREC1 does not meet the specs as the word ekey= is in not in elements2. INREC2 does meet the specs so it blanks the data following ekey= and moves the data it found to the end of the array. The thing to keep in mind is that I have 550 columns and I have to check 10 of those for 4 different words. If found I must blank what follows those words and then move the data I blanked to the end of the array.

You can strip out the values while moving them. From what you describe, I'd ignore the columns (unless it's possible for those key2= patterns to appear in other columns where you want to ignore them). So you could use something like this to get the value for key1, strip it out, and append it to the end of the line:

open my $in,  '<', 'infile'  or die $!; # open input file
open my $out, '>', 'outfile' or die $!; # open output file
while(my $line = <$in>){
  chomp $line;                       # remove newline
  if( $line =~ s/key1=([^&\s]+)// ){ # capture value in $1 while 
                                     #   replacing with empty string
    $line .= " key1=$1";             # append key and value to line
  }
  print $out "$line\n";              # print line to output file
}
close $in;
close $out;
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That will do one find/replace/copy, so you can repeat the if loop while changing the key?= to do multiple ones.