There is no problem at all. Canon has 2 distinct mirrorfree systems for 2 distinct market segments:
* small, light, inexpensive, APS-C = EOS M / EF-M ... with option to use all EF and EF-S lenses
* large, expensive, FF = EOS R / RF ... with option to use all EF and EF-S lenses
In reality there is no "upgrade path" from M to R needed. The habit of buying EF lenses in the past was only because the focal lengths were not available in EF-S mount, because they could not be made any smaller or less expensive for APS-C image circle.
Current owners of Rebels, xxD, 7D/II mirrorslappers plus any assortment of EF/EF-S glass have a whole number of options and "upgrade paths" within Canon EOS ecosystem, depending on their priorities and budgets
1. continue with crop DSLR for a few more years
a) wait for upcoming 7D III [there will be one; 2019] and continue with DSLR for a few more years
b)wait for upcoming 90D [there *might* be one; 2020?]
2. go mirrorfree APS-C with EOS M system; all EF-/EF-S lenses remain fully usable, no need to buy EF-M unless desired
a) "downsize" to EOS M50 [now]
b) wait for upcoming EOS M5 II which *should be* a mirrorfree 90D [2019]
3. go mirrorfree FF with EOS R system, all EF lenses fully usable, EF-S in crop mode; no need to buy RF, unless desired
a) EOS R [now]
b) wait for lower-end, less expensive EOS R FF body [2019]
c) wait for higher-end EOS R bodies - hi rez ["mirrorfree 5DS/R II" [2019]
c) "mirrorfree 1D-X III" [spring 2020]
No problem for Canon or their customers whatsoever. Replace EF/EF-S / add RF lenses when desired and available.
Many Canon customers will also keep EOS M/EF-M when they buy into RF - as a smaller, lighter, less conspicuous, less expensive secondary system.
For almost all users, EF-M / RF lenses not being interchangeable is "no real issue in real life".