Upload file to Sharepoint from external software

Hi testingprofile2345 

you should not have a general problem with more that 5000 items if you upload files to a document library. 

Either some of your columns have settings like "enforce unique values" enabled (that might result in an error on a list with more that 5000 items).
-> I would check that and decide if that setting is necessary

Or the software does more that just upload the file (like setting some metadata afterwards) in a way that is not compatible with more than 5000 items in a list.
-> I would ask the software vendor if they have an idea why this is happening

You could also create a new document library and have the import process upload the files there (Like a drop off library). Then move these files from there to your library using i.e. a power automate flow.  This might even give you the possibility to partition your data into more than one document library later.

Best Regards,
Sven