Sometime within the past two weeks (and very probably as of 5 February when Family Tree DNA (FTDNA) began accepting uploads from the 23andMe v5 test), FTDNA made a change in the formatting of the file users receive when they download their raw autosomal DNA (Family Finder) test results. This has been reported to cause issues uploading the data to other testing companies like MyHeritage, but seems not to be a concern at GEDmatch.
The new file format is sorted by reference sequence ID (RSID) number. These numbers are unique across all chromosomes and reference a specific allele. Previously the FTDNA files—as are those from AncestryDNA and MyHeritage—were sorted by chromosome number first, then by physical position on the human genome map. One advantage of the new format is that allele values at each location are now split into two separate data fields, or columns, where previously they were a single data element (e.g., AA, AG, CT, GT).
The material data seem not to have changed, although some comparisons of raw data downloaded 30 days ago and this week are indicating a minimal number of SNP comparison difference, on the order of 15,000 RSIDs. It seems unlikely FTDNA will expend any resources to modify the format to be backwardly-compatible with MyHeritage. If you have uploads of new FTDNA data pending and incomplete elsewhere, the only course of action now seems to be to wait until the receiving parties can adapt to the new FTDNA format.