See this page in the users guide: Personal Synonyms
Based on that, I made a chromosome synonyms file: MySyns.txt
KlingonChr1 chr1 Chr1
KlingonChr2 chr2 Chr2
KlingonChr3 chr3 Chr3
KlingonChr4 chr4 Chr4
KlingonChr5 chr5 Chr5
And I made an example bed file by taking segments from the A_thaliana gene annotations and replacing the chromosome names: exBed.bed
KlingonChr5 550034 552647 AT5G02490.1 0 - 550295 552565 0 2 2009,296, 0,2317,
KlingonChr5 553744 556442 AT5G02500.1 0 - 554054 556334 0 2 2052,322, 0,2376,
KlingonChr5 553744 556442 AT5G02500.2 0 - 554054 556334 0 3 697,965,322, 0,1087,2376,
KlingonChr5 558284 559235 AT5G02502.1 0 - 558603 558711 0 2 427,94, 0,857,
KlingonChr5 560134 560860 AT5G02510.1 0 + 560134 560860 0 3 273,177,90, 0,356,636,
etc.
I loaded my synonyms file as chromosome synonyms, and restarted IGB. Now I expect that if I open exBed.bed in IGB, it will treat these entries as if they were unchanged, recognizing that KlingonChr5 is equivilent to Chr5. But instead it is creating entire new chromosomes to display the KlingonChr annotations.