It happened to me with Comrade in a run. I had 38/40 of his killquest finished and then it was at Red Eye Boss. I was distracted and the crystal bot got destroyed during the boss battle.

Comrade's kill quest was reset to 0/40 after that which had me really surprised because I remember the killquest with Blaze and Fassie if I recall right had it saved with Blurs and Blobs if you went down/quit the run early. Only Comrade's quest has reset upon reload.

I cannot tell if it is a Comrade specific problem or if it is because during boss level your quests are overwritten with "beat boss" as goal. 

Files here: https://d.kuku.lu/c6ra33nxs

I was playing solo and at no time my game crashed.
The player log from back then I cannot provide, since there are only two saved in ..\AppData\LocalLow\AMPLITUDE Studios\ENDLESS Dungeon

Maybe best to check with those who do the debugging why player logs are only two saved but diagnostics are eight and backups are eight. It is inconsistence.

I also find it weird why they are put in an entire different place - the Temporary Files folder could be also renamed into Diagnostic Files folder. At least right now it gives the impression it is not meant to be persistence.

Reported on Steam