After closing and restarting CCS, changes to Formats or Q-values in Debug Watch are lost.
CCS version = 4.1.3.00038
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You are right, there is an issue in CCS 4.1.3 with preserving changes to Q-value formats in some scenarios. We are tracking this in defect # SDSCM00037694. Please feel free to track the status of this issue via the SDOWP link in my signature.