The annotation qualifiers are present in a form of key-value pairs. If you need to rename the annotation qualifiers (their key), call the command 

edit annotation_qualifier <MapSetId|path> [-t|-d]

This will first list all available qualifiers for a given map set and ask to pick the qualifier to rename.

PS> edit annotation_qualifier 2
Map set: /Rice-platinum standard/Os GJ-temp: IRGSP-1.0 (Nipponbare)
Qualifiers with example values:

Track 'FGENESH gene models':
[0]         Parent ( 56,150 records) : gene10_1
[1]           note ( 36,928 records) : gi|10086415|gb|AAG12481.1|AC037197_6 Unknown protein [Oryza sativa Japonica Group]

Track 'Gene models':
[2]           Name ( 71,475 records) : OsIRGSP-1.0_01T0000100.1
[3]         Parent ( 71,475 records) : OsIRGSP-1.0_01G0000100
[4]           _AED ( 71,475 records) : 0.00
[5]            _QI ( 71,475 records) : 0|-1|0|1|-1|0|1|0|62
[6]          _eAED ( 71,475 records) : 0.00

Track 'Gnomon gene models':
[7]           Name ( 40,881 records) : XM_015755112.1
[8]           gene ( 40,881 records) : LOC107275246
[9] model_evidence ( 40,881 records) : Supporting evidence includes similarity to: 1 EST
[10]        product ( 40,881 records) : (+)-delta-cadinene synthase isozyme XC1-like

Track 'MSU gene models':
[11]             ID ( 66,338 records) : ChrSy.fgenesh.gene.1
[12]           Note ( 66,338 records) : 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase protein, putative, expressed

Type the line [number] with qualifier to edit: 11
Edit qualifier name: geneId
Rename qualifier from ID to geneId? (Y/N) Y
Renamed 66,338 qualifier names

In case the test mode is used (-t), the program will count how many qualifiers will be affected by the renaming operation.

Once the renaming is done, the search index for the corresponding track will be rebuilt.