We have observed a similar behavior in our workflow: after opening an IDML file, it had a SWOP profile as document profile and no longer the original ISOcoated_v2.
The remedy for us is the following procedure: the InDesign with which the IDML file is opened must have a configured color management (i.e. do not leave it in the default setting). The safest way has proven to be to synchronize the color management via Bridge. Afterwards, the output color profiles have been preserved.
We have observed a similar behavior in our workflow: after opening an IDML file, it had a SWOP profile as document profile and no longer the original ISOcoated_v2.
The remedy for us is the following procedure: the InDesign with which the IDML file is opened must have a configured color management (i.e. do not leave it in the default setting). The safest way has proven to be to synchronize the color management via Bridge. Afterwards, the output color profiles have been preserved.