What is the version of xEdit you are using?
SSEEdit 4.0.3 (1CDF3AC7)
SSEEdit 4.1.3a EXTREMELY EXPERIMENTAL (DF87E311)

Describe the bug
If a file adds worldspaces, and it is cleaned with xEdit, the cleaning operation will produce broken files if a refcache is loaded. These broken files have large portions of some of their worldspace's chunks corrupted. For the Soul Cairn and Apocrypha, this is all chunks with X or Z coordinates less than 0. For Darkfall Passage, the coordinates are instead X<-36, Z>16 due to that region's strangely mapped coordinate space.

To reproduce
Steps to reproduce the behavior:

1. Delete SSEEdit Cache
2. Restore uncleaned file (either by reinstalling mod, restoring from backup, or verifying integrity of game cache)
3. Clean file with QuickAutoClean. This cleaned file should work as expected.
4. Restore uncleaned file again.
5. Re-clean file with QuickAutoClean

NOTE: Dawnguard.esm does not behave normally when cleaned, and thus must be manually cleaned using the old Apply Filter for Cleaning method to reproduce the bug.

Expected behavior
The produced file should be identical whether there is, or is not a cache, as the cache should ideally only be speeding up loading times and not modifying behaviour in any way.

Screenshots
DLC01SoulCairn in 0,0 facing toward -1,-1

2 screenshots from DLC1DarkfallPassage (coordinate space is strange here)

DLC2ApocryphaWorld in 0,0 facing toward -1,-1

Additional context
A list of known hashes & sizes for working and broken files in Skyrim Special Edition is as follows:
4.0.3
Update.esm EF461BD9, 18090304 bytes (Working) UNAFFECTED
Dawnguard.esm 955CCA77, 24284359 bytes (Working) C7F92E24, 24341725 bytes (Pass 1 manual cleaning, broken) 43655D8E, 24340112 bytes (Pass 2 manual cleaning, still broken)
HearthFires.esm B384A732, 3681366 bytes (Working) UNAFFECTED
Dragonborn.esm D8C00B93, 64166711 bytes (Working) 3E903FCB, 64357633 bytes (Broken)

4.1.3a
Update.esm F1DD0ADC, 18090423 bytes (Working) 6E8CA420, 18090949 bytes (presumably damaged somehow, but the only added worldspace is a test area that doesn't break)
Dawnguard.esm AD407311, 24284588 bytes (Working) 7EA3B18C, 24341954 bytes (Pass 1 manual cleaning, broken) FA026978, 24340341 bytes (Pass 2 manual cleaning, still broken)
HearthFires.esm D4095EC4, 3681454 bytes (Working) E4B2D2C9, 3681436 bytes (Presumably damaged somehow)
Dragonborn.esm 6973A406, 64166519 bytes (Working) 72D9BB0D, 64357411 bytes (Broken)