1) There is a .csv file (about 2000 lines long, each line containing N,M).
2) There is an .ods spreadsheet with an automatically updated link, 2x5000, linked to the .csv file.
3) With the calc program closed, and no libreoffice processes running, some data in the .csv file are deliberately changed, and the file saved. The new data are verified.
4) When the .ods file is opened, mysteriously, the data in the .csv file are changed to old historic values.
5) If the data in the .csv file is externally changed, and the link updated, the .ods file shows the new data. Both files have the new data.
6) See (4) Both files show up with old historical data anytime the .ods file is opened.
7) When new data is appended to the .csv file, it properly propagates into the .ods file.
9) There is nothing in the spreadsheet that should alter the input data.
Not reproducible using LibO 3.5.2 on Linux, assuming that with "linked" you meant using DDE() spreadsheet formulas, e.g.
Closing as worksforme. If you can reproduce in LibO 3.5.x feel free to reopen and provide a test case document.