First off, you need a good plugin. Try this one: 1) Make a backup of your map
2) Open your map in Entity
3) Duplicate the SNCR tag and give it a different name (such as "scenarios\multi\unused\unused", doesn't matter)
4) Click on both SNCR tags and record the IDENT numbers
5) Open the map in your favorite HEX editor
6) Search for the original IDENT value (remember to reverse the Hex digits)
ex: E1780003 (Ascension) Search for 03 00 78 E1
Ignore the first value found, this is a listing for the SCNR tag (will be followed shortly after by "sgat")
find the second listing and write down the 8 bytes after the IDENT (will be immediately proceded by "rncs")
7) Search for the new IDENT value (reversed again)
Write down the 8 bytes following it's IDENT value.
8) Exchange the 8 byte values between the two tags
ex (IDENTs in Bold):
BEFORE:
orig: 03 00 78 E1 98 C4 1B 80 88 7D 00 00
new: 98 11 1D F3 AC FE 55 80 1C 80 00 00
AFTER EXCHANGE:
orig: 03 00 78 E1 AC FE 55 80 1C 80 00 00
new: 98 11 1D F3 98 C4 1B 80 88 7D 00 00
9) Load the map up in Entity again
10) Clone your chunks as usual in the original SCNR tag (notice the offset will now have changed)
11) Sign your map
Here's the idea behind it. Cloning chunks tends to screw up your map, especially in the SNCR tag, so we make a duplicate of the tag, which relocates it to the end of the map. However, H2 loads the first SCNR tag, so we make the first pointer in the index point to the new tag and the new pointer point to the old tag. Now when we clone chunks, no other meta (other than the UGH!) get shifted, therefore reducing the chance of corrupting the map. Usually, because it is the 3rd tag listed, almost ALL other meta gets moved and any incorrect plugins can brick the map. So if you have issues with this, then chances are we need to do some more work with the SNCR plugin as no others are being touched.
Obviously this will add extra size to your map, but the SCNR tag in Ascension is only 32kb, so

*Note* This should have no issues being done for any other tag as well. I would recommend doing each tag in it's entirety first, then move on to the next tag, so each tag is at the end of the map and not effecting other tags.