I thing that there is now something wrong within your datamodel - like any association between the tables are broken and/or any joins have duplicated a lot of records and/or there are now additionally fields/tables causing synthetic keys or circular loops or something similar - therefore take a look on the datamodel if there is something different as expected.
To @marcus_sommer point, something had to have become corrupted in the QVW file etc., since you have reloaded and it is fine now, whatever it was is likely lost at this point. It could have been something within the meta data of the file etc., but no way to tell at this point. Ensure all utilities running on the server have exceptions for the QVW files etc. to ensure other processes are not trying to do anything to the files while being opened or saved etc. Best I can offer at this point.
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Such things could be also caused by changes within the data. Quite often the used fields aren't explicitly defined else the loads are made with something like: load * from AnySource; But if there is now an important field missing or reverse there are some extra ones it could lead to a variety of errors and/or unexpected behaviour.
Further if any load-parts are conditional - if any records/fields/values exists do this else that and similar stuff - or if section access is used changes within the data, the user or the environment could have an impact.
Therefore again my suggestion to start your trouble-shooting with a check of the datamodel.