The problem is due to a couple of bugs in the chromatogram library code. The root cause is that there are proteins in your documents that have the same sequence but different name / labels. For example:
Some documents have the protein "HPRR5000256" which has the same sequence as "QPrEST_Adiponectin_HPRR5000256" in another document.
The document with "QPrEST_Adiponectin_HPRR5000256" was uploaded first. And then a document with "HPRR5000256" was uploaded. I would have expected this to cause a conflict since the proteins have the same sequence. But due to the bug, the conflict was not reported. So, now the library had both proteins "HPRR5000256" and "QPrEST_Adiponectin_HPRR5000256".
Next, another document with "HPRR5000256" was uploaded, and this time, there was a conflict since the library already has a protein with the same name. When you try to resolve conflicts, all library proteins with the same sequence as "HPRR5000256" are listed in the UI. You will notice that there are two rows for "HPRR5000256". The conflict UI also needs to be fixed, by the way. The protein names in the "Current Library Proteins" cannot be read. Trying to resolve the conflicts fails with an error message is not helpful at all! Sorry about that.
I assume you don't want both "HPRR5000256" and "QPrEST_Adiponectin_HPRR5000256" in your library.
I will fix the bugs and we can, hopefully, have the server updated in the next few weeks. In the mean time, the workaround is to remove some of the older, single protein documents that have protein names that are not the same as the newer documents. I think if you delete the following documents, you should be able to get this folder to a working state.
QPrEST_ PEDF_HPRR4340066_2nd digestion_CE_2020-02-18_11-29-33.sky.zip
Thanks for using chromatogram libraries and reporting bugs!