You don't have to make it so complicated, DSpace data structures are
very sane as opposed to some other systems. After you replaced the
files in the assetstore, calculate a new MD5 checksum for them and
store it to the bitstream table. Notice that bitstream file name in
asset store is not equal to its checksum. The checksum is in the
bitstream.checksum columns and is indeed MD5.

Don't forget to run index-update after you change the values. Running
the checksum checker is a matter of course, you know that.

Just to comment on the problem with the mappings:
you probably used ItemImport with the replace parameter:
https://wiki.duraspace.org/display/DSDOC3x/Importing+and+Exporting+Items+via+Simple+Archive+Format#ImportingandExportingItemsviaSimpleArchiveFormat-ReplacingItemsinCollection

That one deletes the item and submits a new one. using ItemUpdate
instead might work as expected:
https://wiki.duraspace.org/display/DSDOC3x/Updating+Items+via+Simple+Archive+Format

Regards,
~~helix84

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