Still getting this issue in the latest patch, very similar situation to OP's. Massive duplication of TravelObjectIds blocks, with each event repeating itself thousands of times.
It becomes exponential as the safe file grows to the point that once its over a couple of hundred mb's, the save is unusable:
Here is an except of one of the pieces of data that gets repeated
{
"TravelObjectIds": [
"4a1b57f0-56ee-473b-8f5d-950bdc075713",
"a7d70165-6e64-4ec2-ae53-128f669705e4",
"7b5c52a5-a2f6-427f-a624-c061dc567253",
"ffbce690-479a-4b9a-895a-633b629f3fe6",
"ffbce690-479a-4b9a-895a-633b629f3fe6",
"ffbce690-479a-4b9a-895a-633b629f3fe6"
],
"EventKey": "vesselSOIEntered",
"UT": 32885750.697483897,
"FlightReportArgs": [
"Jool",
"Vall"
]
},
I believe this growth is happening while creating a new save. Events that would generate an autosave (leaving VAB, entering a new SOI, etc) are all taking a really long time to complete (because the save is huge). Watching the new saves grow confirms this theory. In addition, I also notice an associated spike in RAM usage with the game using over 11gb's at one point just to write a new Save File, before dropping back to a more respectable 5gb while actually playing the game