Assuming you sync directly to Strava and not via another service; then Change your recording device to source elevation from GPS then they will be default use their DEM elevation model data.
If you are using a RFLKT+ on an iphone your probably better off using Wahoo Fitness app (free) versus runkeeper for cycling.
I use Cyclemeter, but my data is in Runkeeper - it's complicated.
Back a couple years when I started my weight loss trip I was using Lose-It for calorie tracking. I started cycling on an old mountain bike and just used Runkeeper, which syncs with Lose-it automagically. After several months and 30+ pounds lost, I got a roadbike, rflkt, and tried the wahoo app, which can sync to Runkeeper. It failed so I switched to Strava. I setup Strava and Tapiriik to sync the Strava data to Runkeeper to sync to Lose-it. Strava also failed, so I switched to Cyclemeter, which hasn't failed yet. I still use Runkeeper directly for tracking non-cycling activities like rollerblading, but those are a lot more rare since my cycling obsession took over.
Strava now syncs with Lose-It, but the integration is poor from what I understand.
FWIW - the failures are from riding in full sun in 98 degree weather - the phone will occasionally overheat and reboot. Most apps don't recover well from that, but Cyclemeter does.
So back to the elevation... If a rise doesn't hit Strava's magic threshold number of elevation (whatever that is), it records zero because they're trying to smooth noise in the 100's of feet for riders in mountainous regions. Think about it from their perspective - a GPS reading a few feet off in the Rockies is a 1000 foot drop off of a cliff. My 10 foot rises don't compare. If you browse one of my rides, you can see in the elevation profile that Strava does see changes in elevation - they just don't use it. Today's disaster of a ride, for example, Strava shows a low of 22 feet and a high of 40 feet. I know - Larry and Rick are trying not to giggle at my climbing prowess
Here's the rationale from Strava:
https://strava.zendesk.com/entries/20965883-Elevation-for-Your-Activity