If we have a SCORM package stored in SCORM Storage in the SPLMS and we edit the package (for example an XML file in the SCORM package) and re-upload the package do we maintain the information about each users usages or place in the package?

Talking about a SCORM uploaded inside a course yes, it wouldn’t allow to re-upload the package and preserve attempts information. But if we talk about the SCORM Storage this should generally be possible, - to delete a current package and upload the same modified. The important thing is that the file name and title of the package stay the same.

This way it shouldn’t affect attempts of the linked SCORM and it should still work fine.

To keep attempts in both cases (SCORM and Storage) it is possible to modify or replace files via SharePoint Designer:
 - if you open the site and navigate to All files >SCORM Storage > the package;
 - if you open the site and navigate to All files > Scorms > your SCORM package > SCORM folder. There is a zipped package of SCORM and unpacked files of it. You can leave the zipped package as is, but replace the xml and related files there, see screenshot:

NOTE: There are usually no zipped packages inside SCORMs in ScormsStorage.

There is also a way to replace files in SCORM package without SharePoint Designer but with the help of Windows Explorer. Mind that Windows Explorer should be opened under Teacher's (Site collection administrator's) account. See animated example:

NOTE: SCORM resources are cached so your change will be applied in 10 mins. To force the change immediately you can perform IISRESET on the server(s).

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