What is the version of xEdit you are using?
SSEEdit 4.1.3f EXTREMELY EXPERIMENTAL (4AC3F164) starting session 2021-04-05 19:11:39

Describe the bug
This counter (REFR\Bound Data\XRMR - Header\Linked Rooms Count) exists (at least) in FO3, FNV, TES5, FO4 and FO76. It counts the number of linked rooms (REFR\Bound Data\Linked Rooms).
If the counter is wrong, the CK will misbehave. I haven't tested what the game does.
CK behavior is as follows:

• More linked rooms than the counter -> the CK will discard the extraneous rooms
• Fewer linked rooms than the counter -> the CK will discard the entire subrecord structure (REFR\Bound Data, i.e. XRMR/LNAM/INAM/XLRM)

To reproduce
Steps to reproduce the behavior:

1. Create a record with Bound Data (e.g. by copying 00105028 in TES5)
2. Add linked rooms, but do not update the linked rooms counter
3. Resave in the CK, observe that it has either corrected the counter or discarded the entire subrecord structure

Expected behavior
The counter should be updated automatically when you add or remove linked rooms.

Screenshots

(After changing counter to 2 and resaving in the CK)